COSYES-PUBLICATIONS

CONFINED MOLECULAR SYSTEMS: THE NEW GENERATION OF MATERIALS

NATIONAL RESEARCH PROJECT GRANT NUMBER: PID2020-117605GB-I00

(1 September 2021 - 31 August 2025)

PUBLICATIONS (team's members marked in boldface):

 

Abstract: Novel highly selective synthesis techniques have enable the production of atomically precise monodisperse metal clusters (AMCs) of subnanometer size. These AMCs exhibit ‘molecule-like’ structures that have distinct physical and chemical properties, significantly different from those of nanoparticles and bulk material. In this work, we study copper pentamer Cu5 clusters as model AMCs by applying both density functional theory (DFT) and high-level (wave-function-based) ab initio methods, including those which are capable of accounting for the multi-state multi-reference character of the wavefunction at the conical intersection (CI) between different electronic states and augmenting the electronic basis set till achieving well-converged energy values and structures. After assessing the accuracy of a high-level multi-multireference ab initio protocol for the well-known Cu3 case, we apply it to demonstrate that bypiramidal Cu5 clusters are distorted Jahn-Teller (JT) molecules. The method is further used to evaluate the accuracy of single-reference approaches, finding that the coupled cluster singles and doubles and perturbative triples CCSD(T) method delivers the results closer to our ab initio predictions and that dispersion-corrected DFT can outperform the CCSD method. Finally, we discuss how JT effects and, more generally, conical intersections, are intimately connected to the fluxionality of AMCs, giving them a ‘floppy’ character that ultimately facilitates their interaction with environmental molecules and thus enhances their functioning as catalysts.

The Front Cover shows a two-dimensional representation of a conical intersection causing a Jahn-Teller distortion that removes the degeneracy of two electronic states. The lowest-energy potential energy surface features close-lying multi minima and saddle points for bypiramidal Cu5 structures. As a result, Cu5 clusters exhibit fluxional motion, a characteristic enhancing their performance as catalysts. Cover design by Katarzyna Krupka. More information can be found in the Research Article.

  • COVER PROFILE: Alexander O. Mitrushchenkov and María Pilar de Lara-Castells*, "High-level ab initio evidence of bipyramidal Cu5 clusters as fluxional Jahn-Teller molecules". DOI: 10.1002/cphc.202300637

“In order to explain the enhancement of catalytic activities in atomic metal clusters, the concept of ‘structural fluxionality’ has been frequently invoked…” This and more about the story behind the front cover can be found in the Research Article at 10.1002/cphc.202300317.

  • María Pilar de Lara-Castells,* Félix G. Requejo,* Arturo M. López-Quintela* and co-workers, "Stability and Reversible Oxidation of Sub-Nanometric Cu5 Metal Clusters: Integrated Experimental and Theoretical Modeling". Chemistry A European Journal 29 (2023) e202301517. COVER FEATURE: DOI: 10.1002/chem.202302209.

Abstract: Sub-nanometer metal clusters have special physical and chemical properties, significantly different from those of nanoparticles. However, there is a major concern about their thermal stability and susceptibility to oxidation. In situ X-ray Absorption spectroscopy and Near Ambient Pressure X-ray Photoelectron spectroscopy results reveal that supported Cu5 clusters are resistant to irreversible oxidation at least up to 773â€ÂÂÂ…K, even in the presence of 0.15â€ÂÂÂ…mbar of oxygen. These experimental findings can be formally described by a theoretical model which combines dispersion-corrected DFT and first principles thermochemistry revealing that most of the adsorbed O2 molecules are transformed into superoxo and peroxo species by an interplay of collective charge transfer within the network of Cu atoms and large amplitude “breathing” motions. A chemical phase diagram for Cu oxidation states of the Cu5-oxygen system is presented, clearly different from the already known bulk and nano-structured chemistry of Cu.

 

Abstract: The very recent development of highly selective techniques making possible the synthesis and experimental characterization of subnanometric (subnanometer-sized) metal clusters (even single atoms) is pushing our understanding far beyond the present knowledge in materials science, driving these clusters as a new generation of quantum materials at the lower bounds of nanotechnology. When the size of the metalcluster is reduced to a small number of atoms, the d-band of the metal splits into a subnanometric d-type molecular orbitals network in which all metal atoms are interconnected, with the inter-connections having the length of a chemical bond (1-2 Å). These molecular characteristics are at the very core of the high stability and novel properties of the smallest metal clusters, with their integration into colloidal materials interacting with the environment having the potential to further boost their performance in applications such as luminescence, sensing, bioimaging, theranostics, energy conversion, catalysis, and photocatalysis. Through the presentation of very recent case studies, this Feature Article is aimed to illustrate how first-principles modelling, including methods beyond the state-of-the-art and an interplay with cutting-edge experiments, is helping to understand the special properties of these clusters. Moreover, it will be discussed how superfluid helium droplets can act both as nanoreactors and carriers to achieve the synthesis and surface deposition of metal clusters. This concept will be illustrated through the quantum simulation of the helium dropletassisted soft-landing of a single Au atom onto a titanium dioxide (TiO2) surface. Next, it will be shown how the application of first-principles methods has disclosed the fundamental reasons why subnanometric Cu5 clusters are resistant to irreversible oxidation, and capable of increasing and extending into the visible region the solar absorption of TiO2 and augmenting its efficiency for photo-catalysis beyond a factor of four, also considering the decomposition and photo-activation of CO2 as a prototypical (photo-)catalytic reaction. Finally, I will discuss how the modification of the same material with subnanometric Ag5 clusters has converted it into a ``reporter" of a surface polaron property as well as a novel two-dimensional polaronic material.

 

Abstract: Experimental and theoretical work has delivered evidence of the helium nanodroplet-mediated synthesis and soft-landing of metal nanoparticles, nanowires, clusters, and single atoms on solid supports. Recent experimental advances have allowed the formation of charged metal clusters into multiply charged helium nanodroplets. The impact of the charge of immersed metal species in helium nanodroplet-mediated surface deposition is proved by considering silver atoms and cations at zero-temperature graphene as the support. By combining high-level ab initio intermolecular interaction theory with a full quantum description of the superfluid helium nanodroplet motion, evidence is presented that the fundamental mechanism of soft-deposition is preserved in spite of the much stronger interaction of charged species with surfaces, with high-density fluctuations in the helium droplet playing an essential role in braking them. Corroboration is also presented that the soft-landing becomes favored as the helium nanodroplet size increases.

Abstract: Recent advances in synthesis and characterization methods have enabled the controllable fabrication of atomically precise metal clusters (AMCs) of subnanometer size that possess unique physical and chemical properties, yet to be explored. Such AMCs have potential applications in a wide range of fields, from luminescence and sensing to photocatalysis and bioimaging, making them highly desirable for further research. Therefore, there is a need to develop innovative methods to stabilize AMCs upon surface deposition, as their special properties are lost due to sintering into larger nanoparticles. To this end, dispersion-corrected density functional theory (DFT-D3) and ab initio molecular dynamics (AIMD) simulations have been employed. Benchmarking against high-level post-Hartree–Fock approaches revealed that the DFT-D3 scheme describes very well the lowest-energy states of clusters of five and ten atoms, Cu5 and Cu10. AIMD simulations performed at 400 K illustrate how intrinsic defects of graphene sheets, carbon vacancies, are capable of confining individual Cu5 clusters, thus allowing for their stabilization. Furthermore, AIMD simulations provide evidence on the dimerization of Cu5 clusters on defect-free graphene, in agreement with the ab initio predictions of (Cu5)n aggregation in the gas phase. The findings of this study demonstrate the potential of using graphene-based substrates as an effective platform for the stabilization of monodisperse atomically precise Cu5 clusters.

  • Berta Fernández* and María Pilar de Lara-Castells,* "Meta-stability through intermolecular interactions protecting the identity of atomic metal clusters: ab initio evidences in (Cu5-Cu5) (n < 3) cases". Physical Chemistry Chemical Physics 24 (2022) 26992-26997. This article is part of the themed collections: Stability and properties of new-generation metal and metal-oxide clusters down to subnanometer scale and 2022 PCCP HOT Articles

Abstract:  Recent developments in new synthesis techniques have allowed the production of precise monodisperse metal clusters composed of a few atoms. These atomic metal clusters (AMCs) often feature a molecule-like electronic structure, which makes their physical and chemical properties particularly interesting in nanotechnology. Regarding potential applications, there is a major concern about the sintering of AMCs in nanoparticles due to the loss of their special properties. In this work, multireference ab initio theory is applied to demonstrate the formation of coupled AMC–AMC clusters in which the AMC partners maintain their ‘identity’ to a large extent in terms of their initial structures and atomic Mulliken charges, and their further oligomerization.

  • Jaime Garrido-Aldea and María Pilar de Lara-Castells,* "Aggregation and support effects in the oxidation of fluxional atomic metal clusters. The paradigmatic Cu5 case". Physical Chemistry Chemical Physics 24 (2022) 24810-24822. This article is part of the themed collection: Stability and properties of new-generation metal and metal-oxide clusters down to subnanometer scale.

Abstract: The recent development of new synthesis techniques has allowed the production of monodisperse metal clusters composed of a few atoms. Follow-up experimental spectroscopic characterization has indicated the stability of these atomic metal clusters (AMCs). Despite the common assumption that the occurrence of an irreversible oxidation becomes more likely as the cluster size decreases, its quenching and reversible nature has been experimentally identified in the particular case of Cu5 clusters, making them paradigmatic. This work aims to address the influence of aggregation and the effects of a chemically inert carbon-based support on the oxidation of AMCs, considering the case of Cu5 as a model system. For this purpose, we present an extended first-principles study of the oxidation of Cu5–Cu5 and circumpyrene-supported Cu5, comparing it with that of unsupported Cu5, and combine dispersion-corrected density-functionals, first principles thermochemistry, and ab initio molecular dynamics (AIMD) simulations within an adiabatic approach. Our results indicate that a molecular chemisorption/desorption model is sensible upon consideration of aggregation and support effects in such a way that the predicted (p–T)-phase diagrams do not differ significantly from those obtained for unsupported Cu5. We also provide insights into the decoupling of the Cu5–Cu5 dimer into Cu5 sub-units through activated fluxional rotational motion, upon heating, as well as the adsorption of multiple O2 molecules at high oxygen gas pressures. Furthermore, numerical evidence shows the likelihood of a support-mediated mechanism leading to the dissociation of chemisorbed peroxo O22− species, delivering states with very similar energies to those characterized by molecular chemisorption. A Boltzmann-weighted average of the free energies of formation is computed as well, coming up with a diagram of the dominant copper oxidation states as a function of temperature and oxygen gas pressure.

 

Abstract: The electronic structure of subnanometric clusters, far off the bulk regime, is still dominated by molecular characteristics. The spatial arrangement of the notoriously undercoordinated metal atoms is strongly coupled to the electronic properties of the system, which makes this class of materials particularly interesting for applications including luminescence, sensing, bioimaging, theranostics, energy conversion, catalysis, and photocatalysis. Opposing a common rule of thumb that assumes an increasing chemical reactivity with smaller cluster size, Cu5 clusters have proven to be exceptionally resistant to irreversible oxidation, i.e., the dissociative chemisorption of molecular oxygen. Besides providing reasons for this behavior in the case of heavy loading with molecular oxygen, we investigate the competition between physisorption and molecular chemisorption from the perspective of nonadiabatic effects. Landau–Zener theory is applied to the Cu5(O2)3 complex to estimate the probability for a switching between the electronic states correlating the neutral O2 + Cu5(O2)2 and the ionic O2– + (Cu5(O2)2)+ fragments in a diabatic representation. Our work demonstrates the involvement of strong nonadiabatic effects in the associated charge transfer process, which might be a common motive in reactions involving subnanometric metal structures.

  • María Pilar de Lara-Castells* and Salvador Miret-Artés. "A subnanometric material reveals new quantum-chemical insights into surface polarons". Europhysics News 53 (2022) 7-9

Abstract: The recent advent of cutting-edge experimental techniques allows for a precise synthesis of monodisperse subnanometric metal clusters composed by just a few atoms, and opens new possibilities for subnanometer science. The decoration of titanium dioxide surfaces with Ag5 atomic clusters has enabled the stabilization of surface polarons and provided new quantum-chemical insights into an electron polarization phenomenon revealed by their formation.

 

  • María Pilar de Lara-Castells* and Alexander O. Mitrushchenkov*.  "Mini Review: Quantum Confinement of Atomic and Molecular Clusters in Carbon Nanotubes". Frontiers in Chemistry 2021, 9, 796890.

Abstract: We overview our recent developments on a computational approach addressing quantum confinement of light atomic and molecular clusters (made of atomic helium and molecular hydrogen) in carbon nanotubes. We outline a multi-scale first-principles approach, based on density functional theory (DFT)-based symmetry-adapted perturbation theory, allowing an accurate characterization of the dispersion-dominated particle–nanotube interaction. Next, we describe a wave-function-based method, allowing rigorous fully coupled quantum calculations of the pseudo-nuclear bound states. The approach is illustrated by showing the transition from molecular aggregation to quasi-one-dimensional condensed matter systems of molecular deuterium and hydrogen as well as atomic 4He, as case studies. Finally, we present a perspective on future-oriented mixed approaches combining, e.g., orbital-free helium density functional theory (He-DFT), machine-learning parameterizations, with wave-function-based descriptions.

  • Alvaro García-Castillo, Andreas W. Hauser, María Pilar de Lara-Castells,*and Pablo Villarreal*. "A Path Integral Molecular Dynamics Simulation of a Harpoon-Type Redox Reaction in a Helium Nanodroplet". Molecules 2021, 26 (19), 5783.

Abstract: We present path integral molecular dynamics (PIMD) calculations of an electron transfer from a heliophobic Cs2 dimer in its (3Σu) state, located on the surface of a He droplet, to a heliophilic, fully immersed C60 molecule. Supported by electron ionization mass spectroscopy measurements (Renzler et al., J. Chem. Phys.2016, 145, 181101), this spatially quenched reaction was characterized as a harpoon-type or long-range electron transfer in a previous high-level ab initio study (de Lara-Castells et al., J. Phys. Chem. Lett. 2017, 8, 4284). To go beyond the static approach, classical and quantum PIMD simulations are performed at 2 K, slightly below the critical temperature for helium superfluidity (2.172 K). Calculations are executed in the NVT ensemble as well as the NVE ensemble to provide insights into real-time dynamics. A droplet size of 2090 atoms is assumed to study the impact of spatial hindrance on reactivity. By changing the number of beads in the PIMD simulations, the impact of quantization can be studied in greater detail and without an implicit assumption of superfluidity. We find that the reaction probability increases with higher levels of quantization. Our findings confirm earlier, static predictions of a rotational motion of the Cs2 dimer upon reacting with the fullerene, involving a substantial displacement of helium. However, it also raises the new question of whether the interacting species are driven out-of-equilibrium after impurity uptake, since reactivity is strongly quenched if a full thermal equilibration is assumed. More generally, our work points towards a novel mechanism for long-range electron transfer through an interplay between nuclear quantum delocalization within the confining medium and delocalized electronic dispersion forces acting on the two reactants.

OTHER COSYES PUBLICATIONS RELATED TO THE TOPICS OF THE PROJECT

Abstract: Non-symmetric poly(diphenylacetylene)s (PDPAs) show a strong relationship between the size of the macromolecules and their electronic circular dichroism (ECD) spectra. Thus, polymers and oligomers of PDPAs with the same screw sense excess show opposite ECD spectra. This is due to the complex nature of the ECD spectra, where the main electronic transitions depend on the degree of polymerization (DP).

  • Enrique M. Cabaleiro-Lago,* Berta Fernández, Roberto Rodríguez-Fernández, Jesús Rodríguez-Otero, Saulo A. Vázquez.* "Functional group corrections to the GFN2-xTB and PM6 semiempirical methods for noncovalent interactions in alkanes and alkenes", The Journal of Chemical Physics 2023, 158, 124106.

Abstract: Analytical corrections were developed to improve the accuracy of the PM6 and GFN2-xTB semiempirical quantum mechanical methods for the evaluation of noncovalent interaction energies in alkanes and alkenes. We followed the approach of functional group corrections, wherein the atom-atom pair corrections depend on the nature of the interacting functional groups. The training set includes 21 alkane and 13 alkene complexes taken from the Donchev et al.'s database [Sci. Data 8, 55 (2021)], with interaction energies calculated at the CCSD(T)/CBS level, and our own data obtained for medium-size complexes (of 100 and 112 atoms). In general, for the systems included in the training and validation sets, the errors obtained with the PM6-FGC and xTB-FGC methods are within the chemical accuracy.

  •   Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago, and Saulo A. Vázquez.* "The PM6-FGC Method: Improved Corrections For Amines and Amides", Molecules 2022, 27, 1678.

Abstract: Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where the FGC acronym, corresponding to Functional Group Corrections, emphasizes the idea that the corrections work for specific functional groups rather than for individual atom pairs. The analytical corrections were derived from fits to B3LYP-D3/def2-TZVP (reference). PM6 interaction energy differences, evaluated for a reduced set of small bimolecular complexes, were chosen as representatives of saturated hydrocarbons, carboxylic, amine and, tentatively, amide functional groups. For the validation, the method was applied to several complexes of well-known databases, as well as to complexes of diglycine and dialanine, assuming the transferability of amine group corrections to amide groups. The PM6-FGC method showed great potential but revealed significant inaccuracies for the description of some interactions involving the –NH2 group in amines and amides, caused by the inadequate selection of the model compound used to represent these functional groups (an NH3 molecule). In this work, methylamine and acetamide are used as representatives of amine and amide groups, respectively. This new selection leads to significant improvements in the calculation of noncovalent interactions in the validation set.

  • Rafael Rodríguez, Elena Rivadulla-Cendal, Manuel Fernández-Míguez, Berta Fernández, Katsuhiro Maeda, Emilio Quiñoa, and Félix Fréire, "Full Control of the Chiral Overpass Effect in Helical Polymers: P/M Screw Sense Induction by Remote Chiral Centers After Bypasing the First Chiral Residue", Angewandte Chemie International Edition 2022, 61, e20229953.

Abstract: In helical polymers, helical sense induction is usually commanded by teleinduction mechanism, where the largest substituent of the chiral residue directly attached to the main chain is the one that commands the helical sense. In this work, different helical structures with different helical senses are induced in a helical polymer [poly-(phenylacetylene)] when the conformational composition of two different dihedral angles of a pendant group with more than two chiral residues is tamed. Thus, while the dihedral angle at chiral residue 1 [(R)- or (S)-alanine], attached to the backbone, produces an extended or bent conformation in the pendant resulting in two scaffolds with different stretching degree, the second dihedral angle at chiral residue 2 [(R)- or (S)-methoxyphenylacetamide] places the substituents of this chiral center in a different spatial orientation, originating opposite helical senses at the polymer that are induced through a total control of the “chiral overpass effect”.

Abstract: The secondary structure of a dissymmetric and chiral poly(diphenylacetylene) (PDPA) is elucidated by combining the data from NMR experiments (regioregular head to tail structure), Raman and IR studies (E configuration of the polyene double bonds), and high-resolution AFM images (helical pitch, packing angle and orientation of the external helix). As a result, an E-transoidal polyene backbone describing three coaxial helices is obtained. Theoretical electronic circular dichroism (ECD) studies of the structure show a good correspondence between experimental and theoretical data and allow one to decipher that the first Cotton band is generated by the poly(diphenylacetylene) core and not only by the polyene backbone. The dynamic behavior of poly-(S)-2 is also demonstrated by a helix inversion effect produced by conformational changes at the pendant groups when annealed in solvents with different donor abilities. This phenomenon is accompanied by an inversion of the circular polarized luminescence of the PDPA (CPL switch).

The 3D-helical structure of a non-symmetric poly(diphenylacetylene) (PDPA) with dynamic circularly polarized luminescence (CPL) is reported in the Research Article by Félix Freire etâ€ÂÂÂ…al. (e202115070). By conformational changes in the pendant group a helix inversion in the PDPA can be initiated, creating a CPL switch.

Abstract: Supramolecular and covalent polymers share multiple structural effects such as chiral amplification, helical inversion, sergeants and soldiers, or majority rules, among others. These features are related to the axial helical structure found in both types of materials, which are responsible for their properties. Herein a novel material combining information and characteristics from both fields of helical polymers, supramolecular (oligo(p-phenyleneethynylene) (OPE)) and covalent (poly(acetylene) (PA)), is presented. To achieve this goal, the poly(acetylene) must adopt a dihedral angle between conjugated double bonds (ω1) higher than 165°. In such cases, the tilting degree (Θ) between the OPE units used as pendant groups is close to 11°, like that observed in supramolecular helical arrays of these molecules. Polymerization of oligo[(p-phenyleneethynylene)n]phenylacetylene monomers (n = 1, 2) bearing L-decyl alaninate as the pendant group yielded the desired scaffolds. These polymers adopt a stretched and almost planar polyene helix, where the OPE units are arranged describing a helical structure. As a result, a novel multihelix material was prepared, the ECD spectra of which are dominated by the OPE axial array.