Millennium Nucleus
Molecular Engineering for Catalysis and Biosensors

What we learned...


Towards Two-Dimensional Superatomic Honeycomb Structure. Evaluation of [Ge9(Si(SiMe3))3]- as Source of Ge9-Cluster Building Blocks for Extended Materials
Alvaro Muñoz-Castro and Keisuke Takahashi
J. Phys. Chem. C, Just Accepted Manuscript [4.509, 2015]
DOI:   10.1021/acs.jpcc.6b10251
Inspired by recent experimental realizations of two-dimensional (2D) metals and alloys, we theoretically investigate plausible formation of new germanium frameworks based on the aggregation of ligand-decorated Ge9 clusters. Here, we explore the formation of single-, double-, and triply connected arrays of species with Zintl-ion core of Ge9 leading to the formation of dimers ([Ge9R2]22-), hexamers ([Ge9R]66–), and two-dimensional arrays ([M3{Ge9}3]; M = Li, Cs). This can be potentially addressed by the controlled removal of ligands from the [Ge9{Si(SiMe3)3}3]- monoanion acting as the source of Ge9 building blocks. Our results reveal that the bonding between different Ge9 cores is favorable and covalent in nature as a localized 2c–2e Ge–Ge exobond. The extended two-dimensional {Ge9} array designed as [M3{Ge9}3] with M = Li, Cs in periodic boundary conditions is energetically stable. The resulting layered Ge-structure has similar stability as that of germanene. It exhibits large pores with radius of 5.23 Å between the three-connected Ge9 clusters. Hence, it can be considered as a the first superatomic honeycomb structure proposed to date. This 2D material exhibit a small band gap in contrast to the 2D germanene which has no such gap. Hence, the two-dimensional Ge9 cluster-based compound would have potential for a tunable bandgap material. The use of Ge-clusters is suggested as an interesting approach to obtain nanomaterials accessing to novel alleotropes.

Doping the Cage. Re@Au11Pt and Ta@Au11Hg, As Novel 18-ve Trimetallic Superatoms Displaying a Doped Icosahedral Golden Cage
Alvaro Muñoz-Castro
Phys. Chem. Chem. Phys., 2016, Accepted Manuscript [4.449, 2015]
DOI:   10.1039/C6CP07519C
Expanding the versatility of well defined clusters, is a major concern in the design of building blocks towards functional nanostructures. W@Au12, is the prototypical binary bare superatomic clusters involving an icosahedral symmetry, which has been discussed in literature, precluding the proposal of several endohedral d-block and f-block elements structures within a golden cage. Here we pursue the construction of a related trimetallic cluster, which has been explored to a lesser extent. Our results expose the great advantages of involving heterocages in the superatom approach, unraveling Re@Au11Pt and Ta@Au11Hg as novel trimetallic candidates. Re@Au11Pt exhibits an electron-deficient element in the cage, and an endohedral atom with an extra electron. In contrast Ta@Au11Hg is conceived with an icosahedral cage with an extra electron, and an electron-deficient endohedral element. These new clusters follow the eighteen valence electron principle, with similar characteristic to its W@Au12 parent. This leads to stable clusters with an electronic structure formally described by the 1s21p61d10 closing shell order, showing an interesting approach to design ternary superatoms, where the variation of valence electrons occurs in both cage and endohedral sites. Moreover, the cage doping appears as a useful approach to further evaluate the formation of magnetic superatoms, and also the construction of larger cluster by fusing different icosahedral structures.

Insights into bonding interactions and excitation energies of 3d–4f mixed lanthanide transition metal macrocyclic complexes
Walter A. Rabanal-Leon, Juliana A. Murillo-Lopez and Ramiro Arratia-Perez
Phys.Chem.Chem.Phys.,2016, 18, 33218-33225 [4.449, 2015]
DOI:   10.1039/c6cp07001a
In this contribution, a computational study of equatorial bound tetranuclear macrocycle (butylene linked) [LnZnII3(HOMBu)]3+ (Ln = La3+, Ce3+) complexes was carried out. Here, the electronic structure, bonding interaction and excitation energies were studied within the relativistic density functional theory framework. From the electronic structure analysis, the frontier molecular orbitals (FMOs) were strongly localized in the d-orbitals of the Zn centers and the f-orbitals of the lanthanide ions. Besides, the inner MOs were found to exhibit a ?-character from the organic part of the macrocyclic chain. EDA-NOCV was used as a tool for evaluating the bonding interaction, taking the trinuclear metallomacrocycle (ZnII3HOMBu) and the lanthanide center as fragments. This analysis showed that the interaction between these fragments was slightly covalent; with this covalency being the result of a charge transfer from the metallomacrocyclic ring to the lanthanide. This phenomenon was observed in the deformation density channels obtained from the EDA-NOCV study; in which ?- and ?-charge transfer was observed. Finally, the TD-DFT study of the excitation energies evidenced three sets of bands: the first set with the highest intensity represented the ligand to metal charge transfer bands; the second set could be attributed to the 3d–4f electronic transitions between the metal centers; and the third set represented the f–f bands found for the open-shell cerium complex. This class of complexes accomplishes the “antenna effect” principle, which states that highly absorptive transition-metal (TM) complexes can be used to enhance the luminescence of poorly emissive systems, and are introduced in this study as self-sensitizer bimetallic d–f systems with potential applications in near infra-red (NIR) technologies.

DFT studies on coordination models for adsorption essays of Cu(II) and Ni(II) solutions in modified silica gel with iminodiacetic groups
Alexander Carreño, Eduardo Schott, Ximena Zarate, Juan Manuel Manriquez, Juan C. Vega, Miguel Mardones, Alan H. Cowley, Ivonne Chavez, Juan P. Hinestroza, Ramiro Arratia-Perez
Chem. Pap. (2016) [1.326, 2015]
DOI:   10.1007/s11696-016-0022-6
Research in functionalized inorganic supports faces special challenges regarding the inmobilization of organic chains and efficient computational methods for the quantum chemical modeling of coordination compounds. The silylant 3-cloropropyltriethoxysilyl (R1) was anchored over silica gel in anhydrous conditions, in order to react with diethyl Iminodiacetate (DIDA) to obtain modified silica gel (R2), which was hydrolized in basic conditions previously synthesized and characterized by SBET, TGA and FTIR spectroscopy to obtain iminodiacetic acid groups IDA to prepare an modified inorganic support (R3) that is able to get hands on metals from the first transition series such as copper and nickel. The obtained experimental values showed that the functionalized grade of R3 corresponds to 0.1598 mmol of the nitrogen indicated that the adsorbed Cu(II) or Ni(II) have the stoichiometry for both cation of 1:1. Based on this relation, the three different structures were proposed to carry out the computational studies using density functional theory (DFT) in its LDA and PW91 with the TZP slater type basis set. The primary coordination sphere of copper(II) or nickel (II) ion in R3 are optimized, structural parameters are calculated, vibrational bands are assigned and energy gaps of frontier orbital (HOMO–LUMO) have been calculated. The calculated results reproduced the experimental data with good agreement. An energy decomposition analysis (EDA) of the different models proposed here was performed and suggest a 1:1 coordination form.

Doping the Superatom with p-Elements: The Role of p-Block Endohedral Atoms in Bonding and Optical Properties of E@Au24(SR)18 (E = Si, Ge, Sn, and Pb) from Relativistic DFT Calculations
Johanna Camacho Gonzalez and Alvaro Muñoz-Castro
J. Phys. Chem. C, 2016, 120 (47), 27019–27026 [4.509, 2015]
DOI:   10.1021/acs.jpcc.6b04943
Expanding the versatility of well-defined clusters seeking distinctive physical and chemical behavior in a rational manner is a relevant issue in the design of functional nanostructures. Superatomic clusters through the prominent Au25(SR)18 aggregate offer an ideal template and robust framework to gain understading of the different behavior gained by the inclusion of different endohedral dopant atoms. Our results allow to gain more insights into the role of group XIV elements for both optical and bonding, revealing characteristic patterns to be expected in their low-energy UV-spectrum. The bonding shows an extension of the regular s-type interaction observed in [Au@Au24(SR)18]? to a more extended and covalent interaction given by s- and p-type interaction when the central atom is replaced by a group XIV elements, which can be expected of other endohedral p-block elements. In addition, the role of the spin–orbit coupling into the electronic and optical properties is discussed in terms of the new selection rules required by such regime. The characteristic optical and bonding patterns resulting from the p-element endohedral doping of the Au25(SR)18 superatom shed light into the rational variation of the molecular properties upon inclusion of an endohedral p-block element.

Au102+ and Au6X42+ clusters: Superatomic molecules bearing an SP3-hybrid Au6 core
Alvaro Muñoz-Castro, R. Bruce King
J. Quantum Chem. 2016. [2.184, 2015]
DOI:   10.1002/qua.25331
Au102+ and Au6X42+ clusters: Superatomic molecules bearing an SP3-hybrid Au6 core The octahedral Au6 core is explored for the formation of novel SP3-hybrid superatomic molecules by considering Au102+ and Au6X42+ clusters (X = F, Cl, Br, I). The bonding between the four capping atoms and the Au6 core requires a combination of 1S and 1P shells of the core leading to a set of four equivalent hybrid orbitals. Thus, combining the superatom concept with both the Lewis structure model and VSEPR theory contributes to the rationalization of structure and bonding in metal clusters. For example, our results consider the Au6X42+ clusters as analogues of the simplest perhalogenated hydrocarbon, CX4.

Evaluation of Hollow Golden Icosahedrons: Bonding and Spherical Aromatic Properties of [Au11E]3- Superatoms (E=Se and Te) from Relativistic DFT calculations, Persistent Structures?
Alvaro Muñoz-Castro
Chem. Phys. Chem. 2016, 17, 1-7 [3.138, 2015]
DOI:   10.1002/cphc.201600906
Two novel clusters were proposed according to the superatom model involving a favorable inclusion of Se and Te into a Au12 cage leading to [Au11E]3- clusters. Such structures retain a hollow gold-based icosahedron with spherical aromatic character, according to the 18-valence electron rule. Interestingly, it is shown that despite the favorable electronic structure and aromatic behavior, the titled structure is further found to be a local minimum in the potential surface, which exhibits a planar isomer as a plausible candidate for the lowest-energy structure. The proposed strategy employed to vary the electron count of the cage is useful for the further design of novel spherical aromatic superatoms and ligand-protected clusters, for which the main variation is generated directly in the surface of the cluster, in addition to the extensive formation of endohedral clusters with different heteroatoms.

Tiara-like Complexes acting as Iodine Encapsulating Agents: The Role of M···I Interactions in [M(μ-SCH2CO2Me)2]8?I2 (M = Ni, Pd, Pt) Inclusion Compounds
Miguel Ponce-Vargas and Alvaro Muñoz-Castro
J. Phys. Chem. C, 2016, 120 (41), 23441–23448 [4.509, 2015]
DOI:   10.1021/acs.jpcc.6b08643
A proposed series of tiara-like complexes [M(?-SCH2CO2Me)2]8 (where M = Ni, Pd, Pt) are here studied through DFT methodologies prompted by the synthesis of the palladium parent and their potential application in iodine encapsulation from spent nuclear fuel. Their hollow structure with a suitable cavity size, and the presence of several transition-metal centers capable to directly interact with an I2 molecule through noncovalent forces, make them attractive inclusion agents. Herein, an energy decomposition analysis reveals that forces responsible for keeping the guest molecule in the inner cavity are mainly electrostatic; a remarkable feature given, in principle, the neutral nature of both the host and guest species, offering us an interesting study case where the electronic cloud distortion of the binding sites and iodine atoms can be estimated and related to the intensity of the host–guest interactions. Our results shed light into the application of the nickel tiara-like host as an alternative to the reported [Pd(μ-SCH2CO2Me)2]8 system. This research can be useful for further evaluation of nickel-based iodine sequestering agents prior to engaging in explorative synthesis efforts.

Evaluation of Bonding, Electron Affinity, and Optical Properties of M@C28 (M = Zr, Hf, Th, and U): Role of d- and f-Orbitals in Endohedral Fullerenes from Relativistic DFT Calculations
Alvaro Muñoz-Castro and R. Bruce King
Journal of Computational Chemistry 2016 [3.648, 2015]
DOI:   10.1002/jcc.24518
The experimentally characterized endohedral metallic fullerenes involving the small C28 cage, has shown to be able to encapsulate zirconium, hafnium, and uranium atoms, among other elements. Here, we explore the formation and nature of concentric bonds from purely d- to f-block elements, given by Zr, Hf, and uranium, along a borderline metal between such blocks, thorium. We explore the interplay of d- and f-orbitals in the chemistry of the early actinides, where the features of a d- or f-block metal can be mixed. Our results indicate that the bonding of Th@C28 involves contributions from both d- and f-type bonds, as characteristic of this early actinide element. Even uranium in U@C28, also exhibits a contribution from d-type bonds in addition to its relevant f-block character. Electron affinity and optical properties were evaluated to gain more insights into the variation of these molecular properties in this small endohedral fullerene, along Zr, Hf, Th, and U. The current results, allows to unravel the role of (n - 1)d and (n - 2)f orbitals in confined elements ranging from d- to f-blocks, which can be useful to gain a deeper understanding of the bonding situation in other endohedral species.

Catalytic aspects of metallophthalocyanines adsorbed on gold-electrode. Theoretical exploration of the binding nature role
Sebastián Miranda-Rojas, Paulina Sierra-Rosales, Alvaro Muñoz-Castro, Ramiro Arratia-Pérez, José Heráclito Zagal, and Fernando Mendizábal
Phys. Chem. Chem. Phys., 2016,18, 29516-29525 [4.449, 2015]
DOI:   10.1039/C6CP06156G
The need of deeper insights regarding the inner working of catalysts represents a current challenge in the search of new ways to tune their activities towards new chemical transformations. Within this field, metallophthalocyanines-based (MPc) electrocatalysis has gained tremendous attention due to their versatility, low cost, great stability and excellent turn-over properties. In this concern, here we present a quantum chemical study of the formation of supramolecular complexes based on the adsorption of MPcs on gold substrates, and the effect of the substrate on their electrocatalytic properties. For this purpose, we used iron- (FePc), cobalt- (CoPc) and copper-phthalocyanines (CuPc). To model the gold surface we used two gold clusters of different sizes, given by Au26 and Au58 accounting for gold electrode Au(111) surface. Thus, both electronic and binding strength features of the adsorption process between the complexes were analyzed in detail in order to gain a deeper description of the nature of the MPc–Au(111) formation, by using Density Functional Theory (DFT) calculations, at the PBE and TPSS levels including the dispersive contribution according to the Grimme approach (D3). Our results show that dispersion forces rule the MPc–gold interaction, with binding strengths ranging between 61 and 153 kcal mol?1, in agreement to the reported experimental data. To provide a detailed picture of our findings we used the non-covalent interactions index (NCIs) analysis, which offers additional chemical insights regarding the forces that control their interaction strength. Finally, our calculations revealed that among the three MPcs, CuPc required less energy for its oxidation. However, the removal of the electron involves a tremendous decrease of the MPc–gold surface interaction strength thus suggesting its desorption, which would prevent the required reversibility of the redox reaction, explaining its low performance observed experimentally.

Electronic structure and optical properties calculation of Zn-porphyrin with N-annulated perylene adsorbed on TiO2 model for dye-sensitized solar cell applications: A DFT/TD-DFT study
Katherine Paredes-Gil, Fernando Mendizabal, Dayán Páez-Hernández, Ramiro Arratia-Pérez
Computational Materials Science 126 (2017) 514–527 [2.086, 2015]
DOI:   10.1016/j.commatsci.2016.09.042
The current work scrutinizes the chemical behavior of a set of promissory dyes, the Zn-porphyrins with N-annulated Perylene, WW3m-WW8m, within the most important steps in the solar cell: photoexcitation, electron injection and dye regeneration. The photoexcitation step was studied through TD-DFT framework, finding that the most intense band in WW4m, WW6m-WW8m corresponds to the electronic transition of the frontier orbitals HOMO-LUMO. Among these, WW6m is highlighted, because the electronic density of the LUMO is localized over the anchoring group. Therefore, the presence of two ethynylene spacers in the WW6m porphyrin originate an enhancement in the light absorption. On the other hand, we analyze the electron injection modelling two (mono and bidentate) adsorbing modes in WW3m@TiO2-WW8m@TiO2 using DFT (B3LYP+D3) calculations. Adsorption energies show that WW3m@TiO2-WW8m@TiO2 are coordinated in bidentate mode. In this sense, to analyze the density of states (DOS) we found that WW6m@TiO2 present the narrowest band gap (1.53 eV), promoting an easy electron injection, which could explain the origin of the highest overall efficiency of the solar cell for this porphyrin. Finally, dye regeneration , was studied through the free energy associated, ?Gregen, the values are between ?6.61 and ?6.93 eV for WW3m@TiO2-WW8m@TiO2 showing that this step is spontaneous and similar in all porphyrins.

Reactivity Descriptors for the Activity of Molecular MN4 Catalysts for the Oxygen Reduction Reaction
José H. Zagal and Marc T. M. Koper
Angew. Chem. Int. Ed. 2016, 55, 2–14 [11.709, 0]
DOI:   10.1002/anie.201604311
Similarities are established between well-known reactivity descriptors of metal electrodes for their activity in the oxygen reduction reaction (ORR) and the reactivity of molecular catalysts, in particular macrocyclic MN4 metal complexes confined to electrode surfaces. We show that there is a correlation between the MIII/MII redox potential of MN4 chelates and the M-O2 binding energies. Specifically, the binding energy of O2 (and other O species) follows the MIII-OH/MII redox transition for MnN4 and FeN4 chelates. The ORR volcano plot for MN4 catalysts is similar to that for metal catalysts: catalysts on the weak binding side (mostly CoN4 chelates) yield mainly H2O2 as the product, with an ORR onset potential independent of the pH value on the NHE scale (and therefore pH-dependent on the RHE scale); catalysts on the stronger binding side yield H2O as the product with the expected pH-dependence on the NHE scale. The suggested descriptors also apply to heat-treated pyrolyzed MN4 catalysts.

Calculations of the light absorption spectra of porphyrinoid chromophores for dye-sensitized solar cells
Raúl Mera-Adasme, Wen-Hua Xu, Dage Sundholm and Fernando Mendizabal
Phys. Chem. Chem. Phys., 2016, Advance Article [4.449, 0]
DOI:   10.1039/c6cp04627d
Solar power is a strong alternative to the currently used fossil fuels in order to satisfy the world's energy needs. Among them, dye-sensitized solar cells (DSSC) represent a low-cost option. Efficient and cheap dyes are currently needed to make DSSCs competitive. Computational chemistry can be used to guide the design of new light-absorbing chromophores. Here, we have computationally studied the lowest excited states of ZnPBAT, which is a recently synthesized porphyrinoid chromophore with high light-absorption efficiency. The calculations have been performed at ab initio correlated levels of theory employing second-order coupled clusters (CC2) and algebraic diagrammatic construction using second order (ADC(2)) methods and by performing density functional theory (DFT) calculations using the time-dependent DFT (TDDFT) approach for excitation energies. The ultraviolet-visible (UV-vis) spectrum calculated at the ADC(2) and CC2 levels agrees well with the experimental one. The calculations show that ZnPBAT has six electronic transitions in the visible range of the absorption spectrum. The ab initio correlated calculations and previously reported experimental data have been used to assess the performance of several well-known density functionals that have been employed in the present TDDFT study. Solvent effects have been estimated by using the conductor-like screening model (COSMO). The influence of the addition of a TiO2 cluster to the chromophore systems has also been investigated. The results indicate that both CAM-B3LYP and Becke's “half-and-half” (BHLYP) density functionals are appropriate for the studies of excitation energies in the blue range of the visible spectrum for these kinds of porphyrinoid chromophores, whereas the excitation energies of the Q band calculated at the ab initio correlated level are more accurate than those obtained in the present TDDFT calculations. The inclusion of solvent effects has a modest influence on the spectrum of the protonated form of the studied chromophores, whereas solvent models are crucial when studying the absorption spectrum of the anionic chromophore. The calculated UV-vis spectrum for the chromophore anion is not significantly affected by attaching a TiO2 cluster to it.

D6h-Au42 Isomer: A Golden Aromatic Toroid Involving Superatomic ?-Orbitals that Follow the Hückel (4n+2)π rule
Alvaro Muñoz-Castro
Chem. Phys. Chem. 2016, 17, 1-6 [3.138, 2015]
DOI:   10.1002/cphc.201600864
Recently, it has been shown that the superatom concept is intimately connected to relevant tools of great chemical significance, such as the Lewis structure model and the VSEPR theory, which has been employed to understand hybridized and dimeric-like molecules. This suggests a potential rational construction of superatomic clusters mimicking more complex structures. Here, we extend another well-employed concept to the superatomic clusters, to construct a novel Au42 isomer with resemblance to cyclic aromatic molecules. It is shown that the Hückel (4n+2)π rule is ready to be applied, predicting aromatic behavior latterly supported by the favorable evaluation of the induced shielding cone formation. The D6h isomer of Au42 described here exhibits inherent characteristics mimicking aromatic hydrocarbon rings, displaying ?-superatomic orbitals and related properties. This new cluster is the first member of the superatomic clusters family to exhibit an aromatic &pi-electron system.

U@C36. Is there enough room for a second uranium?
A. Muñoz-Castro
RSC Adv., 2016,6, 78176-78180 [3.289, 2015]
DOI:   10.1039/C6RA15471A
The feasible obtention of U2@C36 as a small endohedral bimetallofullerene is evaluated. Our analysis indicates that U2@C36 is a plausible candidate with a U–U bond length of 2.27 Å. The current observation opens the quest for the hypothetical prediction of other small endohedral bimetallofullerenes and their possible experimental characterization.

Multiscale Approach to the Study of the Electronic Properties of Two Thiophene Curcuminoid Molecules
Alvaro Etcheverry-Berríos, Ignacio Olavarría, Mickael L. Perrin, Raúl Díaz-Torres, Domingo Jullian, Ingrid Ponce, José H. Zagal, Jorge Pavez, Sergio O. Vásquez, Herre S. J. van der Zant, Diana Dulic, Núria Aliaga-Alcalde, and Monica Soler
Chem. Eur. J. 2016, 22, 1-12 [, 0]
DOI:   10.1002/chem.201601187
We studied the electronic and conductance properties of two thiophene–curcuminoid molecules, 2-thphCCM (1) and 3-thphCCM (2), in which the only structural difference is the position of the sulfur atoms in the thiophene terminal groups. We used electrochemical techniques as well as UV/Vis absorption studies to obtain the values of the HOMO–LUMO band gap energies, showing that molecule 1 has lower values than 2. Theoretical calculations show the same trend. Self-assembled monolayers (SAMs) of these molecules were studied by using electrochemistry, showing that the interaction with gold reduces drastically the HOMO–LUMO gap in both molecules to almost the same value. Single-molecule conductance measurements show that molecule 2 has two different conductance values, whereas molecule 1 exhibits only one. Based on theoretical calculations, we conclude that the lowest conductance value, similar in both molecules, corresponds to a van der Waals interaction between the thiophene ring and the electrodes. The one order of magnitude higher conductance value for molecule 2 corresponds to a coordinate (dative covalent) interaction between the sulfur atoms and the gold electrodes.

Theoretical study of aromatic-antiaromatic pairs as material in organic solar cells of double light harvesting
Iván Martinez, Eduardo Schott, Ivonne Chávez, Juan Manuel Manríquez, Ximena Zarate
Chem. Phys. Lett. 2016, 659, 31–35 [1.860, 2015]
DOI:   10.1016/j.cplett.2016.06.079
Molecular light harvesting components of organic solar cells containing antiaromatic and aromatic molecules as organic semiconductors were studied. We found that antiaromatic molecules with indacene core can act as acceptors looking for new options to assemble donor/acceptor interfaces. This is supported by their properties such as molecular orbitals energies, rigid fused core that could promote π-π intermolecular interactions imparting ordered nanostructures, that let high charge mobility thanks to their properly low reorganization energy and the optimum energy offsets of the donor/acceptor interfaces. It was found that pentacene might be an excellent donor and the benzo[g]benz[6,7]indeno[1,2-b]fluorene could act as an acceptor.

Shedding Light on the Nature of Host–Guest Interactions in PAHs-ExBox4+ Complexes
Glaucio R. Nagurniak, Giovanni F. Caramori, Renato L. T. Parreira, Pedro A. S. Bergamo, Gernot Frenking, and Alvaro Muñoz-Castro
J. Phys. Chem. C, 2016, 120 (28), 15480–15487 [4.509, 2015]
DOI:   10.1021/acs.jpcc.6b04844
Host–guest (HG) systems formed by polycyclic aromatic hydrocarbons and ExBox4+ are suitable models to gain a deeper understanding of π–π interactions, which are fundamental in supramolecular chemistry. The physical nature of HG interactions between ExBox4+ (1) and polycyclic aromatic hydrocarbons (PAHs) (2-12) is investigated at the light of the energy decomposition (EDA-NOCV), noncovalent interactions (NCI), and magnetic response analyses. The EDA-NOCV results show that the dispersion forces play a crucial role in the HG interactions in PAHs⊂ExBox4+ complexes. The HG interaction energies are dependent on both the size of the PAH employed and the number of π-electrons in the guest molecules. The parallel face-to-face arrangement between HG aromatic moieties is also fundamental to maximize the dispersion interaction and consequently for the attractive energy which leads to the inclusion complex formation.

Density functional study on Keggin heteropolyanions containing fifth period main group heteroatoms
Francisca Clavería-Cádiz, Ramiro Arratia-Pérez, Desmond MacLeod-Carey
Polyhedron 117 (2016) 478–486 [2.108, 2015]
DOI:   10.1016/j.poly.2016.06.035
In this article, a serie of density functional theory (DFT) calculations were carried out on Keggin heteropolyanions [XM12O40]n- (X = Sn(IV), Sb(V) and Te(VI); M = Mo and W; n = 2,3,4) to analyze their molecular structure, vibrational spectra and electronic structure. The energy and composition of the frontier orbitals resemble those containing internal heteroatoms of preceding periods. We found that the diameter of the encapsulated internal {XO4} subunit varies as X does, while {M12O36} size and distances remain almost constant along the series. Vibrational modes calculations show that exist a dependency of the frequency and the anionic charge, nature of the heteroatom X and calculation methodology. Energy decomposition analysis of the {XO4}–{M12O36} interaction shows a predominant ionic character due to the high charge of the {XO4} anionic subunit. COSMO solvation model enabled us to compare heteropolyanions with different total charges. Our results suggest the possibility that these Keggin anions should be stable, being a new challenge for synthetic inorganic chemists.

Fluorescence probes for prokaryotic and eukaryotic cells using Re(CO)3+ complexes with an electron withdrawing ancillary ligand
A. Carreño, M. Gacitúa, J. A. Fuentes, D. Páez-Hernández, J. P. Peñaloza, C. Otero, M. Preite, E. Molins, W. B. Swords, G. J. Meyer, J. Manuel Manríquez, R. Polanco, I. Chávez, and R. Arratia-Pérez
New J. Chem., 2016, 40, 7687 [3.277, 2014]
DOI:   10.1039/C6NJ00905K
Research in fluorescence microscopy presents new challenges, especially with respect to the development of new metal-based fluorophores. In this work, new fac-[Re(CO)3(bpy)L]PF6 (C3) and fac-[Re(CO)3(dmb)L]PF6 (C4) complexes, where L is an ancillary ligand, E-2-((3-amino-pyridin-4-ylimino)-methyl)-4,6-di-tert-butylphenol, both exhibiting an intramolecular hydrogen bond, have been synthesized for use as preliminary probes for fluorescence microscopy. The complexes were characterized using chemical techniques such as UV-vis, 1H-NMR, TOCSY, FT-IR, cyclic voltammetry, mass spectrometry (EI-MS 752.22 M+ for C3 and 780.26 M+ for C4) and DFT calculations including spin–orbit effects. The electron withdrawing nature of the ancillary ligand L in C3 and C4 explains their electrochemical behavior, which shows the oxidation of ReI at 1.84 V for C3 and at 1.88 V for C4. The UV-vis absorption and emission properties have been studied at room temperature in acetonitrile solution. The complexes show luminescent emission with a large Stokes shift (λex = 366 nm, λem = 610 nm for C3 and λex = 361 nm, λem = 560 nm for C4). The TDDFT calculations suggest that an experimental mixed absorption band at 360 nm could be assigned to MLCT (d(Re) → π*(dmb)) and LLCT (π(L) → π*(dmb)) transitions. We have also assessed the cytotoxicity of C3 and C4 in an epithelial cell line (T84). We found that 12.5 μg ml-1 of C3 or C4 is the minimum concentration needed to kill 80% of the cell population, as determined by neutral red uptake. Finally, the potential of C3 and C4 as biological dyes for use in fluorescent microscopy was assessed in bacteria (Salmonella enterica) and yeasts (Candida albicans and Cryptococcus spp.), and in an ovarian cancer cell line (SKOV-3). We found that in all cases, both C3 and C4 are suitable compounds to be used as fluorescent dyes for biological purposes. In addition, we present evidence suggesting that these rhenium(I) tricarbonyl complexes may be also useful as differential fluorescent dyes in yeasts (Candida albicans and Cryptococcus spp.), without the need for antibodies.

Magnetic response properties of gaudiene – a cavernous and aromatic carbocage
M. Rauhalahti, A. Muñoz-Castro and D. Sundholm
Phys. Chem. Chem. Phys., 2016,18, 18880-18886 [4.449, 2014]
DOI:   0.1039/C6CP03808E
A spherical and cavernous carbocage molecule exhibiting faces with larger ring sizes than regular fullerenes is a suitable species for investigating how molecular magnetic properties depend on the structure of the molecular framework. The studied all-carbon gaudiene (C72) is a highly symmetrical molecule with three- and four-fold faces formed by twelve membered rings. Here, we attempt to unravel the magnetic response properties of C72 by performing magnetic shielding and current density calculations with the external magnetic field applied in different directions. The obtained results indicate that the induced current density flows mainly along the chemical bonds that are largely perpendicular to the magnetic field direction. However, the overall current strength for different directions of the magnetic field is nearly isotropic differing by only 10% indicating that C72 can to some extent be considered to be a spherical aromatic molecule, whose current density and magnetic shielding are ideally completely isotropic. The induced magnetic field is found to exhibit long-range shielding cones in the field direction with a small deshielding region located perpendicularly to the field outside the molecule. The magnetic shielding is isotropic inside the molecular framework of C72, whereas an orientation-dependent magnetic response appears mainly at the exterior of the molecular cage.

Green synthesis of polysaccharides-based gold and silver nanoparticles and their promissory biological activity
Daniela A. Geraldo, Paula Needham, Nancy Chandia, Ramiro Arratia-Perez, Guido C. Mora, Nicolás A. Villagra
Biointerface Res. Appl. Chem., 2016, 6(3) [, 0]
This paper demonstrates a green approach for the synthesis of gold and silver nanoparticles using polysaccharides extracted f macroseaweed as reducing agents. The formation of Au Electron Microscopy (TEM). TEM analysis of both polysaccharides polysaccharides (alginate or carrageenan) not only influence the morphology and the sizes of the nanostructures but also avo aggregation of them. The biological activity of these eco organisms such as Pseudomonas aeruginosa and well-known inorganic reducing agent, sodium citrate (SC). Furthermore, hemolytic activity was also tested showing that the polysaccharides-based metallic nanoparticles (Ps prepared using SC. These results strongly suggest that these Ps infections.

The impact of endohedral atoms on the electronic and optical properties of Au25(SR)18 and Au38(SR)24
A. Muñoz-Castro
Phys. Chem. Chem. Phys., 2016, 18, 31419 [4.449, 2015]
DOI:   10.1039/c6cp02691e
An understanding of the rational modification of the optical properties of gold nanoparticles allows us to explore their versatility as molecular-sized materials. We show from theoretical relativistic calculations that such properties can be tuned efficiently by varying the architecture of the central core from endohedral to hollow structures in thiolate-protected clusters derived from two prototypical gold clusters, namely, Au25(SR)18 and Au38(SR)24. Our results estimate the feasible variation of the absorption spectrum driven by the modification of frontier levels due to the removal of the endohedral atom, leading to smaller gaps between occupied and low-lying unoccupied levels. This reveals a characteristic consequence for hollow counterparts given by a red-shift in energy of the optical properties. Hence, the formation of hollow derivatives can be a useful strategy for the fine-tuning of such properties. Future work will extend this observation to larger clusters, and allow gleaning knowledge of the electronic and optical properties in the case of higher order multilayer core nanoparticles.

Book: Electrochemistry of N4 Macrocyclic Metal Complexes
Editors: Jose H. Zagal, Fethi Bedioui
Springer International Publishing 2016, ISBN: 978-3-319-31170-8 (Print) 978-3-319-31172-2 (Online) [, 0]
DOI:   10.1007/978-3-319-31172-2
This new edition describes the state of the art regarding molecular catalysts such as MN4 metal complexes, like porphyrins and phthalocyanines. This volume focuses on the particular case of the electrocatalysis of the reduction of O2 for practical applications in fuel cells and air batteries. Indeed, active and stable materials have been developed in the last 5 years where MN4 catalytic systems can be obtained by the pyrolysis of starting materials that do not necessarily involve MN4 complexes. These latter systems constitute a new class of stable and highly active non-precious metal catalysts for ORR that can replace expensive Platinum containing electrodes. The book also offers future projections and points out new fields of research and development of these non-precious metal catalysts.

Theoretical Aspects of the Reactivity of MN4 Macrocyclics in Electrochemical Reactions
Sebastián Miranda-Rojas, Alvaro Muñoz-Castro, Ramiro Arratia-Pérez, Fernando Mendizábal
Chapter in "Electrochemistry of N4 Macrocyclic Metal Complexes", Springer International Publishing, PISBN 978-3-319-31170-8, OISBN 978-3-319-31172-2, April 2016, pp 143-170 [, 0]
DOI:   10.1007/978-3-319-31172-2_5
We studied the electronic features of different adsorption and catalytic processes of some transition metal macrocyclic complexes (phthalocyanine) with Fe being the usual metal center. For oxygen molecule on iron phthalocyanine (FePc), both end-on and side-on configurations are found to be energetically favorable. However, the end-on adsorption configurations are more stable than side-on configurations. The activation barrier for the O–O bind cleavage for the side-on MN4-O2 configuration is lower than that for the end-on MN4-O2 configuration. On the other hand, we have built theoretical models based on DFT calculations from the formation of self-assembled monolayers (SAM) on a gold substrate and a thiolate ligand as an “anchoring” fragment of metallophtalocyanine, which leads to an interesting charge donation from the 4-aminothiophenol (4-ATP), 4-MP (4-mercaptopyridine) and 1-(4-mercaptophenyl)-2, 6-diphenyl-4- (4-pyridyl)pyridinium tetrafluoroborate (MDPP) towards both gold substrate, Au(111) surface, and phthalocyanine, denoting an effective gold-MPc interaction mediated by the titled anchor ligands. The electrocatalytic studies carried out with Au/4-ATP/FePc and Au/MDPP/FePc electrodes show that the O2 reduction takes place by the transfer of 4-electron to give water in contrast to a 2-electron transfer process observed for the bare gold. Theoretical calculations suggest the importance of the backbonding mechanism into the adduct formation, showing the relevance of the supporting gold surface on the electron-transfer process mediated by anchoring ligands.

On the Role of Heteroatoms into Aromatic Rings. Insights from 10? Main Group Elements Heterorings [(EH)2S2N4]q (E=C, P, B, Si, Al and q=0,-2)
Alvaro Muñoz-Castro, Nickolas D. Charistos and Anastasios G. Papadopoulos
New J. Chem., 2016, Accepted Manuscript [3.086, 2014]
DOI:   10.1039/C5NJ03573B
Inclusion of heteroatoms into a ring skeleton give rise to unique electronic features, which differs from the respective isoelectronic organic counterparts, increasing the versatility of aromatic molecules. Here we evaluate the role of heteroatoms into the electronic and magnetic properties in a number of inorganic 10π-electron eight-member aromatic rings, involving the isoelectronic [(EH)2S2N4]q (E=C, P, B, Si, Al) series, by using density functional methods. The inclusion of different heteroatoms with increasing electronegativity, increases the aromatic behavior in relation to the representative 10π-electron [C8H8]2- organic ring. A deeper analysis on the magnetic response to an applied magnetic field, in terms of individual π-orbital’s contribution, reveals that the differentiation in aromaticity originates from orbitals with major contributions from pz of heteroatom E, whereas the diatropic contributions rise from the S2N4 core remaining similar through the series. Hence, the effect of including a certain type of heteroatom can be addressed in terms of the variation and contribution of each individual π-orbital, starting from the respective organic counterpart, which appears to be a convenient approach. The similar π-aromatic character observed, suggest the proposed hypothetical rings, a feasible structures to explore synthetically. The less aromatic counterpart given by the Al counterpart, should lead to the less stable ring in the series.

Surface on Surface. Survey of the Monolayer Gold-Graphene interaction from Au12 and PAH via Relativistic DFT Calculations
Alvaro Muñoz-Castro, Tatiana Gómez, Desmond MacLeod Carey, Sebastián Esteban Miranda-Rojas, Fernando Mendizabal, Jose H. Zagal, and Ramiro Arratia-Perez
J. Phys. Chem. C, Just Accepted Manuscript [4.772, 2014]
DOI:   10.1021/acs.jpcc.5b12580
Gold-graphene interaction at the interface is evaluated through different polyaromatic hydrocarbons (PAH), accounted by C6H6, C24H12, C54H16 and C96H18, focusing into different energetic terms related to the overall interaction. Our results characterize the neutral gold-PAH interaction nature with 45% of dispersion character, 35% of electrostatic, and 20% of covalent character, suggesting that moderate van der Waals character is mostly involved in the interaction, which increases according to the size of the respective PAH. The resulting surface charge distribution in the graphene model is a relevant parameter to take into account, since the ability of the surface charge to be reorganized over the polycyclic structure in both contact and surrounding regions is important in order to evaluate interactions and different interacting conformations. Our results suggest that for a Au12 contact surface of radius 4.13 Å, the covalent, electrostatic and dispersion character of the interaction are effectively accounted in a graphene surface of about 6.18 Å, as given by circumcoronene, depicting a critical size where the overall interaction character can be accounted.

Insights into metal-ligand and metal-metal interaction in coinage metal triangles. Insights of d10-d10, d10-d8 and d8-d8 contacts from [Au3In(CH3Ndouble bond; length as m-dashCOCH3)3] (n = 2, 4, 6) via relativistic DFT calculations
R. Guajardo Maturana, A. Muñoz-Castro
Chem. Phys. Lett. 2016, 651, 34–38 [1.897, 2014]
DOI:   10.1016/j.cplett.2016.03.013
The successive addition of one, two and three equivalents of iodide to [Au3(CH3Ndouble bond; length as m-dashCOCH3)3], gives rise to the [Au3In(CH3Ndouble bond; length as m-dashCOCH3)3] (n = 2, 4, 6) oxidized systems. Such structures have been studied by using scalar relativistic DFT calculations and TD-DFT. Our results demonstrate a stronger ligand-to-metal charge donation, which increases in covalency. The long metal-metal contacts observed through the series result from the similarly population of bonding, non-bonding and slightly anti-bonding combinations of the 6s-Au atomic shells in the [Au3]n+ core, leading to distances in the range of the sum of their van der Waals radii for all the systems.

On the fused-to-single ring transition in 10π structures. Insights from naphthalene to [10]annulene series
Alvaro Muñoz-Castro
Chem. Phys. Lett. 2016, 650, 60–63 [1.897, 2014]
DOI:   10.1016/j.cplett.2016.02.064
The fused-to-single-ring transition is studied through a 10πe series given the series from naphthalene to [10]annulene. Our results suggest that change occurs at certain structure instead of a gradual transition. In the transition point, given by bicyclo[7.1.0]decapentaene, similar magnetic behavior in comparison to the single ring counterpart is found. The systems can be considered to behave as a whole single aromatic structure where the fused counterparts can be treated as a modification in the aromatic path of a single ring aromatic motif, which can viewed as a useful approach to evaluate the formation of defects or larger-rings in graphene motifs.

Thiolate-protected golden fullerenes. A 32-ve core involving a hollow Au32 cage
M. Rauhalahti, A. Muñoz-Castro and D. Sundholm
RSC Adv., 2016, 6, 21332-21336 [3.840, 2014]
DOI:   10.1039/C5RA27683G
We have computationally investigated the possible formation of large hollow gold nanostructures based on a Au32 core covered with a thiolate layer using relativistic density functional theory calculations. We have found that [Au32@Au12(SR)18]6- is a plausible candidate that retains the structural, electronic and spherical aromatic properties of the Au32 cage of its parent bare Au32 golden fullerene. The study shows that the low-energy part of the optical spectrum can serve as a guide to identify such hollow gold structures among other small-sized gold nanoclusters with similar nuclearities. The low-lying excited states are dominated by 1f → 1g transitions, which significantly distinguish hollow clusters from other nanoclusters, like the prominent [Au25(SR)18]- cluster, whose low-lying excitations are dominated by 1p → 1d transitions. The gold nanoclusters studied here can serve as model compounds for assessing the metallic core size effects on the absorption energies and the influence of the surface structure of the gold core on the cluster properties. The present study suggests that it is also plausible that even larger hollow structures derived from Au42, Au72, and Au92 golden fullerenes can exist.

Improvement of photovoltaic performance by substituent effect of donor and acceptor structure of TPA-based dye-sensitized solar cells
Natalia Inostroza, Fernando Mendizabal , Ramiro Arratia-Perez, Carlos Orellana, Cristian Linares-Flores
Journal of Molecular Modeling, 2016, Online Jan. 7 [1.736, 2014]
DOI:   10.1007/s00894-015-2893-9
We report a computational study of a series of organic dyes built with triphenylamine (TPA) as an electron donor group. We designed a set of six dyes called (TPA-n, where n = 0-5). In order to enhance the electron-injection process, the electron-donor effect of some specific substituent was studied. Thus, we gave insights into the rational design of organic TPA-based chromophores for use in dye-sensitized solar cells (DSSCs). In addition, we report the HOMO, LUMO, the calculated excited state oxidized potential Edye*(eV) and the free energy change for electron-injection ΔGinject(eV), and the UV-visible absorption bands for TPA-n dyes by a time-dependent density functional theory (TDDFT) procedure at the B3LYP and CAM-B3LYP levels with solvent effect. The results demonstrate that the introduction of the electron-acceptor groups produces an intramolecular charge transfer showing a shift of the absorption wavelengths of TPA-n under studies.

Theoretical exploration of seleno and tellurophenols as promising alternatives to sulfur ligands for anchoring to gold (111) materials
Sebastian Miranda-Rojas, Richard Salazar-Molina, Johannes Kastner, Ramiro Arratia-Perez and Fernando Mendizabal
RSC Adv., 2016,6, 4458-4468 [3.840, 2014]
DOI:   10.1039/C5RA21964G
It is widely known that sulfur ligands, such as alkanethiols or phenothiols and their derivatives, are useful anchor systems for gold materials due to the high affinity of sulfur to gold surfaces. In this study we use DFT calculations and a 42-atom gold cluster model to study the interaction between selenophenol and tellurophenol-derivatives with the Au(111) surface to gain information towards potential new gold-based materials. We modulated the interaction strength by controlling the charge transfer process of a particular interaction by chemically modifying the ligands. To obtain a complete analysis, we studied the ligands in their protonated, anionic and radical states aiming to cover the three possibilities in which these may interact with the gold cluster. In order to get a deeper insight into the nature of the interaction we used several analysis techniques such as energy decomposition analysis (EDA), non-covalent interactions (NCI) and natural population analysis (NPA). Our results reveal that tellurium in the anionic state provides complexes of better thermodynamic stability by ∼12.0 kcal mol, when compared with the strongest sulfur-gold complex, also in the anionic state. Furthermore, this indicates that the anionic ligand is probably the dominant state for both selenium and tellurium as observed previously for sulfur. The extent to which the interaction strength could be controlled directly depends on the state of the anchor atom. In our case the anionic state is the most suitable for tuning the interaction. Finally, our main findings suggest that exchanging sulfur with selenium or tellurium involves an important increase of the interaction strength, thus, making these selenophenol and tellurophenol derivatives attractive for the development of new functional materials.

Atomic force microscopy (AFM) and 3D confocal microscopy as alternative techniques for the morphological characterization of anodic TiO2 nanoporous layers
Diego P. Oyarzún, Omar E. Linarez Pérez, Manuel López Teijelo, César Zúñiga, Eduardo Jeraldo, Daniela A. Geraldo, Ramiro Arratia-Perez
Mat. Lett. 2016, 165, 67-70 [2.466, 2014]
DOI:   10.1016/j.matlet.2015.11.087
The morphologic characterization of self-organized TiO2 nanostructures by field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM) was compared with results obtained by both atomic force microscopy (AFM) and 3D confocal microscopy, which were employed as alternative characterization methods. It is demonstrated that AFM with tuning fork configuration (intermittent mode) is also a powerful tool that allows obtaining conclusive information on the morphology of one-dimensional nanostructures. 3D confocal microscopy employed for the first time for obtaining thickness of nanoporous TiO2 films, is a new and powerful method that provides definite information on thickness of the nanostructures. The results employed for the characterization are fairly reliable besides novel and interesting.

Theoretical and experimental characterization of a novel pyridine benzimidazole: suitability for fluorescence staining in cells and antimicrobial properties
Alexander Carreño, Manuel Gacitúa, Juan A. Fuentes, Dayán Páez-Hernández, Carmen Araneda, Ivonne Chávez, Marco Soto-Arriaza, Juan M. Manríquez, Rubén Polanco, Guido C. Mora, Carolina Otero, Wesley B. Swords, and Ramiro Arratia-Pérez
New J. Chem., 2016, 40, 2362-2375 [3.277, 2015]
DOI:   10.1039/C5NJ02772A
Benzimidazoles presenting intramolecular hydrogen bonding interactions have been normally used to better understand the role of H-bonding in biological processes. Here, we present an experimental and theoretical study of a new compound [2,4-di-tert-butyl-6-(3H-imidazo[4,5-c]pyridine-2-yl)phenol]; (B2), a benzimidazole derivate, exhibiting an intramolecular hydrogen bond. B2 was synthesized and characterized by its 1H, HHCOSY, FT-IR and mass spectra (EI-MS 323 M+). The electronic and optical properties of B2 were studied with theoretical calculations using density functional theory (DFT) and time-dependent DFT (TDDFT). B2 showed luminescent emission at room temperature in different solvents, with a large Stokes shift (e.g.; λex = 335 nm; λem = 510 nm in acetonitrile). Also, the quantum yield (φ = 0.21) and theoretical band emission are reported. We found that B2 exhibited a fluorescence emission at around 500 nm in ethanol and in acetonitrile that could be quenched by aqueous solutions of Hg(NO3)2 in the range of micro molar concentrations. Cyclic voltammetry in acetonitrile showed a strong anodic response due to a quasireversible process, with reduction and oxidation waves at -1.28 and -0.47 V vs. SCE. Regarding the biological properties, we assessed the antimicrobial activity of B2 in Salmonella enterica (bacteria), Cryptococcus spp. (yeast), Candida albicans (yeast), Candida tropicalis (yeast) and Botrytis cinerea (mold). To this end, we determined the minimal inhibitory concentration (MIC) (for bacteria and yeasts), the growth inhibition halos (for yeasts), and the inhibition of mycelial growth (for the mold). We observed that B2 exerted an antifungal effect against Cryptococcus spp. and Botrytis cinerea. In addition, due to its fluorescence properties, B2 has proven to be a suitable marker to observe bacteria (Salmonella enterica and an Escherichia coli derivative), yeasts (Candida albicans), and even human cells (SKOV-3 and HEK-293) by confocal microscopy.

Effect of the crystal environment on the optical and magnetic properties of Nd3+ and U3+ ions
Dayán Páez-Hernández
Polyhedron 105 (2016) 35–41 [2.108, 2015]
DOI:   10.1016/j.poly.2015.12.006
Optical, magnetic properties and the low-energy region of the electronic spectra in the Nd3+ and U3+ fluoride complexes embedded in CaF2 have been analyzed. The effect of the local charge compensation by interstitial F- could be evaluated via the crystal field (CF) distortion with respect to the ideal octahedral environment. All the result were obtained with the help of ab initio wave function calculations including spin–orbit coupling (SO) via the MRCI state interaction of scalar relativistic CAS wave functions. The level of theory employed in this work shows a good correlation between the experimental and calculated spectroscopic properties allowing not only the correct determination of the f→f transitions, but also the f→d transitions in the absorption spectra. An analysis of the ground states and the magnetic behavior is performed using crystal-field (CF) models with parameters extracted from the ab initio calculations. The calculated g-factors are in concordance with the experimental data.