Control of the assembly of a cyclic hetero[4]pseudorotaxane from a self-complementary [2]rotaxane.

The synthesis of a ditopic interlocked building-block and its self-assembly into a cyclic dimer is reported herein. Starting from a thread with two recognition sites, a three-component clipping reaction was carried out to construct a bistable [2]rotaxane. A subsequent Suzuki cross-coupling reaction allowed the connection of a second ring to that of the rotaxane, affording a self-complementary ditopic system. NMR studies were carried out to identify a cyclic hetero[4]pseudorotaxane as the main supramolecular structure in solution. Its assembly is the result of a positive cooperativity operating in the hydrogen-bonding-driven assembly of this mechanically interlocked supramolecule, as revealed by computational studies. The increase of the polarity of the solvent allows the disruption of the intercomponent interactions and the disassembly of the hetero[4]pseudorotaxane into the two interlocked units. The disassembly of the cyclic dimer was also achieved through a Diels-Alder reaction over the fumaramide binding site of the thread, triggering the translational motion of the entwined macrocycle to an adjacent glycylglycine-based station and precluding the supramolecular dimerization. The competitive molecular recognition of a guest molecule by one of the self-templating counterparts of the dimer also led to the controlled disassembly of the hetero[4]pseudorotaxane.

Metastable Dianions and Dications.

A theoretical study of metastable dianions and dications has been carried out at the CCSD(T)//MP2 level. MX32- and LX42- (M=Li and Na, L=Be and Mg, X=F and Cl) have been considered as dianions, M3 X2+ (M=Li and Na, X=F and Cl), YH32+ and ZH42+ (Y=F and Cl and Z=O, S) as dications. Minima structures are found in all cases, but they are less stable than the corresponding dissociated pair of mono-ions. The dissociation profile of the molecules in two mono-ions has been explored showing in all cases a maximum that prevent their spontaneous dissociation. The strength and nature of the chemical bond in the dianions and dications have been analyzed with the QTAIM, NBO and LMOEDA method and compared to the corresponding monoanions and monocations.

Unexpected chalcogen bonds in tetravalent sulfur compounds.

In this manuscript we have combined a CSD (Cambridge Structural Database) analysis with theoretical calculations (RI-MP2/def2-TZVP level of theory) to study the importance of polarizability in chalcogen bonding interactions. It is well known that chalcogen bonds are stronger for less electronegative chalcogen atoms, i.e., S < Se < Te, and in the presence of electron-withdrawing substituents at the chalcogen. Herein, we report experimental and theoretical evidence (RI-MP2/def2-TZVP) that the chalcogen bond acceptor (Lewis base) has a preference in some cases for the σ-hole that is opposite to the more polarizable group instead of the more electron withdrawing one, as confirmed by Natural Bond Orbital (NBO) and Bader's theory of "atoms-in-molecules" computational tools.

Cations brought together by hydrogen bonds: the protonated pyridine-boronic acid dimer explained.

According to the Cambridge Structural Database, protonated pyridine-boronic acid dimers exist in the solid phase, apparently defying repulsive coulombic forces. In order to understand why these cation-cation systems are stable, we carried out M06-2X/6-311++G(3df,2pd) electronic structure calculations and used a set of computational tools (energy partitioning, topology of the electron density and electric field maps). The behavior of the charged dimers was compared with the corresponding neutral systems, and the effect of counterions (Br- and BF4-) and the solvent (PCM model) on the binding energies has been considered. In the gas-phase, the charged dimers present positive binding energies but are local minima, with a barrier (16-19 kJ mol-1) preventing dissociation. Once the environment is included via solvent effects or counterions, the binding energies become negative; remarkably, the strength of the interaction is very similar in both neutral and charged systems when a polar solvent is considered. Essentially, all methods used evidence that the intermolecular region where the HBs take place is very similar for both neutral and charged dimers. The energy partitioning explains that repulsion and electrostatic terms are compensated by the desolvation and exchange terms in polar solvents, thus giving stability to the charged dimer.

Influence of the aromatic surface on the capacity of adsorption of VOCs by magnetite supported organic-inorganic hybrids.

It has been recently evidenced that hybrid magnetic nanomaterials based on perylene diimide (PDI) dopamine and iron oxide nanoparticles are useful for the adsorption and determination of volatile organic compounds (VOCs). However, NDI compounds are expensive and difficult to handle compared to smaller size diimides. Therefore, in this manuscript a combined experimental and theoretical investigation is reported including the analysis of the effect of changing the aromatic surface on the ability of these magnetite supported organic-inorganic hybrid nanoparticles (NPs) to adsorb several aromatic and non-aromatic VOCs. In particular, two new hybrid Fe3O4NPs are synthesized and characterized where the size of organic PDI dopamine linker is progressively reduced to naphthalene diimide (NDI) and pyromellitic diimide (PMDI). These materials were utilized to fill two sorbent tubes in series. Thermal desorption (TD) combined with capillary gas chromatography (GC)/flame detector (FID) was used to analyze both front and back tubes. Adsorption values (defined as % VOCs found in the front tube) were determined for a series of VOCs. The binding energies (DFT-D3 calculations) of VOC-Fe3O4NP complexes were also computed to correlate the electron-accepting ability of the arylene diimide (PDI, NDI or PMDI) with the adsorption capacity of the different tubes. The prepared hybrids can be easily separated magnetically and showed great reusability.

Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study.

In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH)(PW11 O39 )]4- (ZrK) have been investigated using the hybrid two-layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392-Glu393 site of HSA is predicted to occur in the rate-limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392-Glu393, Ala257-Asp258, Lys313-Asp314, and Arg114-Leu115) for the hydrolysis of all four sites of HSA. © 2018 Wiley Periodicals, Inc.

Adsorption and Quantification of Volatile Organic Compounds (VOCs) by using Hybrid Magnetic Nanoparticles.

The ability of Fe3 O4 magnetic nanoparticles decorated with perylene bisimides to adsorb aromatic volatile organic compounds (VOCs) is reported. We have used DFT-D3 calculations to anticipate the strong ability of the electron-poor perylene bisimide to form noncovalent complexes with electron-rich aromatic rings belonging to the VOC family. Subsequently, we synthesized a hybrid magnetic nanomaterial based on bisimide perylene dopamine and iron oxide nanoparticles. This material was used to fill a sorbent tube to study its ability to adsorb aromatic VOCs. We connected two tubes in series filled with the hybrid nanoparticles. The analysis of the front and back tubes was performed by thermal desorption (TD) coupled with capillary gas chromatography (GC)/flame ionization detector (FID). Adsorption values (defined as %VOCs found in the back tube) were determined for a series of aromatic VOCs and compared with the DFT binding energies. The tubes can be desorbed and reutilized more than 200 times without losing their properties.

Investigating Polyoxometalate-Protein Interactions at Chemically Distinct Binding Sites.

In this study, a combined molecular docking (rigid and flexible) and all-atom molecular dynamics simulations technique have been employed to investigate interactions of 1:1 Zr-containing Keggin polyoxometalate (ZrK) with four chemically distinct cleavage sites [Arg114-Leu115 (site 1), Ala257-Asp258 (site 2), Lys313-Asp314 (site 3), and Cys392-Glu393 (site 4)] of human serum albumin (HSA). The ZrK-HSA complexations were analyzed using electrostatic potentials, the chemical nature of amino acid residues, binding free energies, and secondary structures as parameters. They suggested that ZrK binds in a rather distinct manner to different cleavage sites, and its association was dominated by hydrogen bonding, both direct and solvent mediated, and electrostatic interactions, as suggested experimentally. The computed binding free interaction energies (-57.5, -24.2, -50.8, and -91.2 kJ/mol for sites 1, 2, 3, and 4, respectively) predicted the existence of one major binding site (site 4) and three minor binding sites (site 1, site 2, and site 3). The strong exothermicity of the binding was also supported by isothermal calorimetry experiments. Additionally, the binding of ZrK did not alter the overall α-helical secondary structure of HSA, which was in line with experimental observation. Furthermore, hydrolysis of the peptide bonds of the substrate was found to retain its overall structure. These results have provided a deeper understanding of the complex ZrK interactions with proteins, and they will lead to the design of the next generation of catalytically active polyoxometalates with improved hydrolytic activities.

Substituent Effects in Multivalent Halogen Bonding Complexes: A Combined Theoretical and Crystallographic Study.

In this manuscript, we combined ab initio calculations (RI-MP2/def2-TZVPD level of theory) and a search in the CSD (Cambridge Structural Database) to analyze the influence of aromatic substitution in charge-assisted multivalent halogen bonding complexes. We used a series of benzene substituted iodine derivatives C6H4(IF4)Y (Y = H, NH2, OCH3, F, CN, and CF3) as Lewis acids and used Cl- as electron rich interacting atoms. We have represented the Hammett's plot and observed a good regression coefficient (interaction energies vs. Hammett's σ parameter). Additionally, we demonstrated the direct correlation between the Hammett's σ parameter and the value of molecular electrostatic potential measured at the I atom on the extension of the C-I bond. Furthermore, we have carried out AIM (atoms in molecules) and NBO (natural bonding orbital) analyses to further describe and characterize the interactions described herein. Finally, we have carried out a search in the CSD (Cambridge Structural Database) and found several X-ray structures where these interactions are present, thus giving reliability to the results derived from the calculations.

Hydrogen Bond versus Halogen Bond in Cation-Cation Complexes: Effect of the Solvent.

Competition between hydrogen- (HB) and halogen-bonded (XB) 4-ammoniumpyridine and halogenammonium (NHn F3-n X+ ; n=0-3; X=F, Cl, Br, and I) cation-cation complexes are explored by means of DFT calculations. HB and XB minima structures are found for all systems in the gas phase. As the number of fluorine atoms increases, the HB complexes are more favored than those of XB. Proton transfer is generally observed in complexes with two, three, or four halogen atoms. The XB complexes evolve from traditional halogen bonds, to halogen-shared complexes, and to ionic complexes as the number of fluorine atoms increases. The dissociation transition states and their corresponding barriers are also characterized; the barriers increase as the number of fluorine atoms increases. The results if solvent effects are considered indicate that, even in an apolar solvent, such as n-hexane, most of the complexes have favorable binding energies. Atoms-in-molecules theory is used to analyze the complexes, and results in good correlations between electron density and total electron energy density (Η) values with the intermolecular bond length. According to the Η values obtained, the covalency of these interactions starts to manifest at distances around 72-74 % the sum of the van der Waals radii of the interacting atoms.

Cation-cation and anion-anion complexes stabilized by halogen bonds.

Stable minima showing halogen bonds between charged molecules with the same sign have been explored by means of theoretical calculations. The dissociation transition states and their corresponding barriers have also been characterized. In all cases, the results indicate that the complexes are thermodynamically unstable but kinetically stable with respect to the isolated monomers in gas phase. A corrected binding energy profile by removing the charge-charge repulsion of the monomers shows a profile similar to the one observed for the dissociation of analogous neutral systems. The nature of the interaction in the minima and TSs has been analyzed using the symmetry adapted perturbation theory (SAPT) method. The results indicate the presence of local favorable electrostatic interactions in the minima that vanish in the TSs. Natural bond orbital (NBO) and "atoms-in-molecules" (AIM) theories were used to analyze the complexes, obtaining good correlations between Laplacian and electron density values with both bond distances and charge-transfer energy contributions E(2). The largest E(2) orbital interaction energies for cation-cation and anion-anion complexes are 561.2 and 197.9 kJ mol-1, respectively.

A thorough anion-π interaction study in biomolecules: on the importance of cooperativity effects.

Noncovalent interactions have a constitutive role in the science of intermolecular relationships, particularly those involving aromatic rings such as π-π and cation-π. In recent years, anion-π contact has also been recognized as a noncovalent bonding interaction with important implications in chemical processes. Yet, its involvement in biological processes has been scarcely reported. Herein we present a large-scale PDB analysis of the occurrence of anion-π interactions in proteins and nucleic acids. In addition we have gone a step further by considering the existence of cooperativity effects through the inclusion of a second noncovalent interaction, i.e. π-stacking, T-shaped, or cation-π interactions to form anion-π-π and anion-π-cation triads. The statistical analysis of the thousands of identified interactions reveals striking selectivities and subtle cooperativity effects among the anions, π-systems, and cations in a biological context. The reported results stress the importance of anion-π interactions and the cooperativity that arises from ternary contacts in key biological processes, such as protein folding and function and nucleic acids-protein and protein-protein recognition. We include examples of anion-π interactions and triads putatively involved in enzymatic catalysis, epigenetic gene regulation, antigen-antibody recognition, and protein dimerization.

Anion Recognition by Pyrylium Cations and Thio-, Seleno- and Telluro- Analogues: A Combined Theoretical and Cambridge Structural Database Study.

Pyrylium salts are a very important class of organic molecules containing a trivalent oxygen atom in a six-membered aromatic ring. In this manuscript, we report a theoretical study of pyrylium salts and their thio-, seleno- and telluro- analogues by means of DFT calculations. For this purpose, unsubstituted 2,4,6-trimethyl and 2,4,6-triphenyl cations and anions with different morphologies were chosen (Cl-, NO3- and BF4-). The complexes were characterized by means of natural bond orbital and "atoms-in-molecules" theories, and the physical nature of the interactions has been analyzed by means of symmetry-adapted perturbation theory calculations. Our results indicate the presence of anion-π interactions and chalcogen bonds based on both σ- and π-hole interactions and the existence of very favorable σ-complexes, especially for unsubstituted cations. The electrostatic component is dominant in the interactions, although the induction contributions are important, particularly for chloride complexes. The geometrical features of the complexes have been compared with experimental data retrieved from the Cambridge Structural Database.

Reconciling experiment and theory in the use of aryl-extended calix[4]pyrrole receptors for the experimental quantification of chloride-π interactions in solution.

In this manuscript we consider from a theoretical point of view the recently reported experimental quantification of anion-π interactions (the attractive force between electron deficient aromatic rings and anions) in solution using aryl extended calix[4]pyrrole receptors as model systems. Experimentally, two series of calix[4]pyrrole receptors functionalized, respectively, with two and four aryl rings at the meso positions, were used to assess the strength of chloride-π interactions in acetonitrile solution. As a result of these studies the contribution of each individual chloride-π interaction was quantified to be very small (<1 kcal/mol). This result is in contrast with the values derived from most theoretical calculations. Herein we report a theoretical study using high-level density functional theory (DFT) calculations that provides a plausible explanation for the observed disagreement between theory and experiment. The study reveals the existence of molecular interactions between solvent molecules and the aromatic walls of the receptors that strongly modulate the chloride-π interaction. In addition, the obtained theoretical results also suggest that the chloride-calix[4]pyrrole complex used as reference to dissect experimentally the contribution of the chloride-π interactions to the total binding energy for both the two and four-wall aryl-extended calix[4]pyrrole model systems is probably not ideal.

Long-range effects in anion-π interactions: their crucial role in the inhibition mechanism of Mycobacterium tuberculosis malate synthase.

The glyoxylate shunt is an anaplerotic bypass of the traditional Krebs cycle. It plays a prominent role in Mycobacterium tuberculosis virulence, so it can be exploited for the development of antitubercular therapeutics. The shunt involves two enzymes: isocitrate lyase (ICL) and malate synthase (GlcB). The shunt bypasses two steps of the tricarboxylic acid cycle, allowing the incorporation of carbon, and thus, refilling oxaloacetate under carbon-limiting conditions. The targeting of ICL is complicated; however, GlcB, which accommodates the pantothenate tail of acetyl-CoA in the active site, is easier to target. A catalytic Mg(2+) unit is located at the bottom of the cavity, and plays a very important role. Recently, the development of effective antituberculosis drugs based on phenyldiketo acids (PDKAs) has been reported. Interestingly, all the crystal structures of GlcB-inhibitor complexes exhibit close contact between the carboxylate of Asp633 and the face of the aromatic ring of the inhibitor. Remarkably, the replacement of the phenyl ring in PDKA by aliphatic moieties yields inactive inhibitors, suggesting that the aromatic moiety is crucial for inhibition. However, the aromatic ring of PDKA is not electron-deficient, and consequently, the anion-π interaction is expected to be very weak (dominated only by polarization effects). Herein, through a combination analysis of the recent X-ray structures of GlcB-PDKA complexes retrieved from the protein data bank (PDB) and computational ab initio studies (RI-MP2/def2-TZVP level of theory), we demonstrate the prominent role of the Mg(2+) ion in the active site, which promotes long-range enhancement of the anion-π interaction.

Thermodynamic characterization of halide-π interactions in solution using "two-wall" aryl extended calix[4]pyrroles as model system.

Herein, we report our latest experimental investigations of halide-π interactions in solution. We base this research on the thermodynamic characterization of a series of 1:1 complexes formed between halides (Cl(-), Br(-), and I(-)) and several α,α-isomers of "two-wall" calix[4]pyrrole receptors bearing two six-membered aromatic rings in opposed meso positions. The installed aromatic systems feature a broad range of electron density as indicated by the calculated values for their electrostatic surface potentials at the center of the rings. We show that a correlation exists between the electronic nature of the aromatic walls and the thermodynamic stability of the X(-)⊂receptor complexes. We give evidence for the existence of both repulsive and attractive interactions between π systems and halide anions in solution (between 1 and -1 kcal/mol). We dissect the measured free energies of binding for chloride and bromide with the receptor series into their enthalpic and entropic thermodynamic quantities. In acetonitrile solution, the binding enthalpy values remain almost constant throughout the receptor series, and the differences in free energies are provoked exclusively by changes in the entropic term of the binding processes. Most likely, this unexpected behavior is owed to strong solvation effects that make up important components of the measured magnitudes for the enthalpies and entropies of binding. The use of chloroform, a much less polar solvent, limits the impact of solvation effects revealing the expected existence of a parallel trend between free energies and enthalpies of binding. This result indicates that halide-π interactions in organic solvents are mainly driven by enthalpy. However, the typical paradigm of enthalpy-entropy compensation is still not observed in this less polar solvent.

On the importance of anion-π interactions in the mechanism of sulfide:quinone oxidoreductase.

Sulfide:quinone oxidoreductase (SQR) is a flavin-dependent enzyme that plays a physiological role in two important processes. First, it is responsible for sulfide detoxification by oxidizing sulfide ions (S(2-) and HS(-)) to elementary sulfur and the electrons are first transferred to flavin adenine dinucleotide (FAD), which in turn passes them to the quinone pool in the membrane. Second, in sulfidotrophic bacteria, SQRs play a key role in the sulfide-dependent respiration and anaerobic photosynthesis, deriving energy for their growth from reduced sulfur. Two mechanisms of action for SQR have been proposed: first, nucleophilic attack of a Cys residue on the C4 of FAD, and second, an alternate anionic radical mechanism by direct electron transfer from Cys to the isoalloxazine ring of FAD. Both mechanisms involve a common anionic intermediate that it is stabilized by a relevant anion-π interaction and its previous formation (from HS(-) and Cys-S-S-Cys) is also facilitated by reducing the transition-state barrier, owing to an interaction that involves the π system of FAD. By analyzing the X-ray structures of SQRs available in the Protein Data Bank (PDB) and using DFT calculations, we demonstrate the relevance of the anion-π interaction in the enzymatic mechanism.

Is the use of diffuse functions essential for the properly description of noncovalent interactions involving anions?

It is commonly assumed that theoretical DFT or ab initio calculations involving anions require the utilization of diffuse functions in order to obtain reliable results. In large systems, the use of diffuse functions in the calculations increases the computational cost and, more importantly, sometimes provokes self-consistent-field (SCF) convergence problems, especially in open shell systems. Nowadays, the popular and often used bases for studying noncovalent interactions are the correlation-consistent polarized basis sets of Dunning and co-workers, denoted as cc-pVXZ (X = D, T, etc.), and the Turbomole def2 basis set family (def2-SVP and def2-TZVP). In this paper we study the effect of the utilization of diffuse functions on the energetic and geometric features of several noncovalent complexes, including hydrogen, halogen, and pnicogen bonding, lithium bonds, anion-π interactions, and van der Waals interactions.

Anion-π interactions involving [MX(n)](m-) anions: a comprehensive theoretical study.

In this manuscript we perform a systematic study on the geometric and energetic features of anion-π complexes, wherein the anion is a metal complex of variable shapes and charges. Such a study is lacking in the literature. For the calculations we used the ab initio RI-MP2/def2-TZVPP level of theory. A search in the Cambridge Structural Database (CSD) provides the experimental starting point that inspired the subsequent theoretical study. The influence of [MX(n)](m-) on the anion-π interaction was analyzed in terms of energetic, geometric, and charge transfer properties and Bader's theory of "atom-in-molecules" (AIM). The binding energy depends on the coordination index, geometric features and different orientations adopted by the metallic anion. The binding mode resembling a stacking interaction for linear, trigonal planar and square-planar anions is the most favorable. For tetrahedral and octahedral anions the most favorable orientation is the one with three halogen atoms pointing to the ring.

Pnicogen-π complexes: theoretical study and biological implications.

The energetic and geometric features of pnicogen-π complexes involving different types of aromatic rings (benzene, trifluorobenzene, hexafluorobenzene and s-triazine) and the heavier pnicogenes (ECl(3), E = As, Sb, Bi) are investigated using theoretical methods (ab initio and DFT-D3). We have analyzed how the interaction energy is affected by the π-acidity of the aromatic moieties and the pnicogen used. In addition, we have found several examples in the Protein Databank where pnicogen-π interactions are present. This likely indicates the potential use of this interaction in the design and synthesis of potential inhibitors of enzymatic reactions. Moreover, in order to know the reliability of the latest version of dispersion termed corrected DFT-D3, we have also compared the energies obtained using the ab initio MP2 method with those obtained using BP86-D3. We have also computed and analyzed the dispersion contribution to the total interaction energy in order to know if it is crucial for the favourable binding. This allows a better understanding of the physical nature of the interaction. Finally, we have used the Bader's theory of "atoms-in-molecules" to demonstrate that the electron density computed at the bond critical point that emerges upon complexation can be used as a measure of bond order in this noncovalent interaction.