P. M. Deya

Bio: P. M. Deya is an academic researcher from Spanish National Research Council. The author has contributed to research in topics: Cooperativity & Ab initio. The author has an hindex of 14, co-authored 22 publications receiving 614 citations. Previous affiliations of P. M. Deya include University of Sheffield & University of Barcelona.

Anion−π Interactions in Bisadenine Derivatives: A Combined Crystallographic and Theoretical Study

Abstract: In this manuscript we report a high-level ab initio study of anion−π interactions involving N9-methyl-adenine, N6-methyl-adenine, N9-methyl-hypoxanthine, a dimer of N9-methyl-adenine, and N9,N9‘-trimethylene-bisadenine. DNA bases like adenine are electron-deficient arenes that are well suited for interacting favorably with anions. We demonstrate that these compounds are able to interact favorably with anions. N9-Methyl-adenine, N6-methyl-adenine, and the dimer of N9-methyl-adenine interact with the anion via the six-membered ring more strongly than adenine due to cooperativity effects between the noncovalent π−π and anion−π interactions. This pattern, i.e., coexistence of π−π and anion−π bonding, is observed experimentally in the solid state. Finally, we report the solid-state characterization of two new compounds N6,N6‘-dimethylene-bisadenine hydrochloride and an outer-sphere complex of protonated N9,N9‘-trimethylene-bishypoxanthine with zinc tetrachloride anion, that exhibit interesting anion−π interact...

DABCO-Induced self-assembly of a trisporphyrin double-decker cage: thermodynamic characterization and guest recognition.

Abstract: This paper describes the thermodynamic characterization of the self-assembly of a Zn trisporphyrin induced by coordination with 1,4-diazabicyclo[2.2.2]octane (DABCO) to form a stable 2:3 double-decker molecular coordination cage that recognizes benzene-1,3,5-tricarboxamides. The self-assembly process has been studied using UV−vis and 1H NMR spectroscopy and quantitatively characterized in terms of a single stability constant that describes the strength of the individual coordination interactions and two effective molarities (EM) that describe the additional stability imparted by intramolecular cyclization. The EM values of the two consecutive cyclic intramolecular interactions are very similar. At micromolar concentrations, the formation of the fully assembled coordination cage is highly favored over the formation of intermediate species stabilized by fewer interactions, and so self-assembly is an all-or-nothing process. In contrast, at millimolar concentrations, the relative stability of intermediate spe...

Coordination Complexes Exhibiting Anion · · ·π Interactions: Synthesis, Structure, and Theoretical Studies

Abstract: The polydentate ligand 2,4,6-tris(dipyridin-2-ylamino)-1,3,5-triazine (dpyatriz) in combination with the Cu(ClO4)2/CuX2 salt mixtures (X− = Cl−, Br−, or N3−) leads to the formation of molecular coordination aggregates with formulas [Cu3Cl3(dpyatriz)2](ClO4)3 (2), [Cu3Br3(dpyatriz)2](ClO4)3 (3), and [Cu4(N3)4(dpyatriz)2(DMF)4(ClO4)2](ClO4)2 (4). These complexes consist of two dpyatriz ligands bridged via coordination to CuII and disposed either face-to-face in an eclipsed manner (2 and 3) or parallel and mutually shifted in one direction. The copper ions complete their coordination positions with Cl− (2), Br− (3), or N3−, ClO4−, and N,N-dimethylformamide (DMF) (4) ligands. All complexes crystallize together with noncoordinate ClO4− groups that display anion···π interactions with the triazine rings. These interactions have been studied by means of high level ab initio calculations and the MIPp partition scheme. These calculations have proven the ClO4−···[C3N3] interactions to be favorable and have revealed ...

Simultaneous Interaction of Tetrafluoroethene with Anions and Hydrogen-Bond Donors: A Cooperativity Study

Abstract: A computational study of the complexes formed by tetrafluoroethylene, C2F4, with anions has been carried out by means of density functional theory (DFT) and second-order Moller-Plesset (MP2) computational methods, up to MP2/aug-cc-pVTZ level. In addition, the possibility of cooperativity in the interaction of anions and hydrogen-bond donors (FH, ClH, and H2O) when interacting with different faces of the C2F4 molecule has been explored. Electron density of the complexes has been analyzed by means of atoms in molecules (AIM) methodology, while natural bond orbital (NBO) methodology has been used to characterize the orbital interaction. In addition, natural energy decomposition analysis (NEDA) has been applied to analyze the source of the interaction. The energetic results indicate that C2F4 is a weaker anion receptor than C6F6, but in combination with the anions, it became a stronger hydrogen acceptor than C2H4. Cooperativity effects are observed in YH·C2F4·X(-) clusters. In C2F4·X(-) complexes the dominant attractive terms are the electrostatic and polarization ones, while in YH·C2F4·X(-) complexes the charge transfer increases significantly, becoming the most important term for most of the FH and ClH complexes studied here.

Energetic vs synergetic stability: a theoretical study.

Abstract: The aim of this manuscript is to define a new concept, namely synergetic stability, which can be useful in systems where the interplay of noncovalent interactions is important. Usually, the stabili...

Supramolecular coordination: self-assembly of finite two- and three-dimensional ensembles.

Abstract: Fascination with supramolecular chemistry over the last few decades has led to the synthesis of an ever-increasing number of elegant and intricate functional structures with sizes that approach nanoscopic dimensions Today, it has grown into a mature field of modern science whose interfaces with many disciplines have provided invaluable opportunities for crossing boundaries both inside and between the fields of chemistry, physics, and biology This chemistry is of continuing interest for synthetic chemists; partly because of the fascinating physical and chemical properties and the complex and varied aesthetically pleasing structures that supramolecules possess For scientists seeking to design novel molecular materials exhibiting unusual sensing, magnetic, optical, and catalytic properties, and for researchers investigating the structure and function of biomolecules, supramolecular chemistry provides limitless possibilities Thus, it transcends the traditional divisional boundaries of science and represents a highly interdisciplinary field In the early 1960s, the discovery of ‘crown ethers’, ‘cryptands’ and ‘spherands’ by Pedersen,1 Lehn,2 and Cram3 respectively, led to the realization that small, complementary molecules can be made to recognize each other through non-covalent interactions such as hydrogen-bonding, charge-charge, donor-acceptor, π-π, van der Waals, etc Such ‘programmed’ molecules can thus be self-assembled by utilizing these interactions in a definite algorithm to form large supramolecules that have different physicochemical properties than those of the precursor building blocks Typical systems are designed such that the self-assembly process is kinetically reversible; the individual building blocks gradually funnel towards an ensemble that represents the thermodynamic minimum of the system via numerous association and dissociation steps By tuning various reaction parameters, the reaction equilibrium can be shifted towards the desired product As such, self-assembly has a distinct advantage over traditional, stepwise synthetic approaches when accessing large molecules It is well known that nature has the ability to assemble relatively simple molecular precursors into extremely complex biomolecules, which are vital for life processes Nature’s building blocks possess specific functionalities in configurations that allow them to interact with one another in a deliberate manner Protein folding, nucleic acid assembly and tertiary structure, phospholipid membranes, ribosomes, microtubules, etc are but a selective, representative example of self-assembly in nature that is of critical importance for living organisms Nature makes use of a variety of weak, non-covalent interactions such as hydrogen–bonding, charge–charge, donor–acceptor, π-π, van der Waals, hydrophilic and hydrophobic, etc interactions to achieve these highly complex and often symmetrical architectures In fact, the existence of life is heavily dependent on these phenomena The aforementioned structures provide inspiration for chemists seeking to exploit the ‘weak interactions’ described above to make scaffolds rivaling the complexity of natural systems The breadth of supramolecular chemistry has progressively increased with the synthesis of numerous unique supramolecules each year Based on the interactions used in the assembly process, supramolecular chemistry can be broadly classified in to three main branches: i) those that utilize H-bonding motifs in the supramolecular architectures, ii) processes that primarily use other non-covalent interactions such as ion-ion, ion-dipole, π–π stacking, cation-π, van der Waals and hydrophobic interactions, and iii) those that employ strong and directional metal-ligand bonds for the assembly process However, as the scale and degree of complexity of desired molecules increases, the assembly of small molecular units into large, discrete supramolecules becomes an increasingly daunting task This has been due in large part to the inability to completely control the directionality of the weak forces employed in the first two classifications above Coordination-driven self-assembly, which defines the third approach, affords a greater control over the rational design of 2D and 3D architectures by capitalizing on the predictable nature of the metal-ligand coordination sphere and ligand lability to encode directionality Thus, this third strategy represents an alternative route to better execute the “bottom-up” synthetic strategy for designing molecules of desired dimensions, ranging from a few cubic angstroms to over a cubic nanometer For instance, a wide array of 2D systems: rhomboids, squares, rectangles, triangles, etc, and 3D systems: trigonal pyramids, trigonal prisms, cubes, cuboctahedra, double squares, adamantanoids, dodecahedra and a variety of other cages have been reported As in nature, inherent preferences for particular geometries and binding motifs are ‘encoded’ in certain molecules depending on the metals and functional groups present; these moieties help to control the way in which the building blocks assemble into well-defined, discrete supramolecules4 Since the early pioneering work by Lehn5 and Sauvage6 on the feasibility and usefulness of coordination-driven self-assembly in the formation of infinite helicates, grids, ladders, racks, knots, rings, catenanes, rotaxanes and related species,7 several groups - Stang,8 Raymond,9 Fujita,10 Mirkin,11 Cotton12 and others13,14 have independently developed and exploited novel coordination-based paradigms for the self-assembly of discrete metallacycles and metallacages with well-defined shapes and sizes In the last decade, the concepts and perspectives of coordination-driven self-assembly have been delineated and summarized in several insightful reviews covering various aspects of coordinationdriven self-assembly15 In the last decade, the use of this synthetic strategy has led to metallacages dubbed as “molecular flasks” by Fujita,16 and Raymond and Bergman,17 which due to their ability to encapsulate guest molecules, allowed for the observation of unique chemical phenomena and unusual reactions which cannot be achieved in the conventional gas, liquid or solid phases Furthermore, these assemblies found applications in supramolecular catalysis18,19 and as nanomaterials as developed by Hupp20 and others21,22 This review focuses on the journey of early coordination-driven self-assembly paradigms to more complex and discrete 2D and 3D supramolecular ensembles over the last decade We begin with a discussion of various approaches that have been developed by different groups to assemble finite supramolecular architectures The subsequent sections contain detailed discussions on the synthesis of discrete 2D and 3D systems, their functionalizations and applications

Aromatic rings in chemical and biological recognition: energetics and structures.

Abstract: This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.