Centro Singular de Investigación en Química Biológica y Materiales Moleculares

This feature review describes the development of catalytic [4+2] and [4+3] cycloadditions of allenes, as efficient and practical methodologies for assembling six and seven-membered cyclic systems. The different methodologies have been classified depending on the type of key reactive intermediate that was proposed in the catalytic cycle.

Very recently, we proposed an automated method for finding transition states of chemical reactions using dynamics simulations; the method has been termed Transition State Search using Chemical Dynamics Simulations (TSSCDS) (E. Martínez-Núñez, J. Comput. Chem., 2015, 36, 222-234). In the present work, an improved automated search procedure is developed, which consists of iteratively running different ensembles of trajectories initialized at different minima. The iterative TSSCDS method is applied to the complex C3H4O system, obtaining a total of 66 different minima and 276 transition states. With the obtained transition states and paths, statistical RRKM calculations and Kinetic Monte Carlo simulations are carried out to study the fragmentation dynamics of propenal, which is the global minimum of the system. The kinetic simulations provide a (three-body dissociation)/(CO elimination) ratio of 1.49 for an excitation energy of 148 kcal mol(-1), which agrees well with the corresponding value obtained in the photolysis of propenal at 193 nm (1.1), suggesting that at least these two channels: three-body dissociation (to give H2 + CO + C2H2) and CO elimination occur on the ground electronic state.

Attachment of alloc protecting groups to the amidine units of fluorogenic DNA-binding bisbenzamidines or to the amino groups of ethidium bromide leads to a significant reduction of their DNA affinity. More importantly, the active DNA-binding species can be readily regenerated by treatment with ruthenium catalysts in aqueous conditions, even in cell cultures. The catalytic chemical uncaging can be easily monitored by fluorescence microscopy, because the protected products display both different emission properties and cell distribution to the parent compounds.

Chiral amplification can be switched ON/OFF to both helical senses by the presence/absence of metal ions in copolymers of poly(phenylacetylene)s.

We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions.

p-Sulfonatocalixarenes are a special class of water soluble macrocyclic molecules made of 4-hydroxybenzenesulfonate units linked by methylene bridges. One of the main features of these compounds relies on their ability to form inclusion complexes with cationic and neutral species. This feature, together with their water solubility and apparent biological compatibility, had enabled them to emerge as one the most important host receptors in supramolecular chemistry. Attachment of hydrophobic alkyl chains to these compounds leads to the formation of macrocyclic host molecules with amphiphilic properties. Like other oligomeric surfactants, these compounds present improved performance with respect to their monomeric counterparts. In addition, they hold their recognition abilities and present several structural features that depend on the size of the macrocycle and on the length of the alkyl chain, such as preorganization, flexibility and adopted conformations, which make these molecules very interesting to study structure-aggregation relationships. Moreover, the recognition abilities of p-sulfonatocalixarenes enable them to be applied in the design of amphiphiles constructed from non-covalent, rather than covalent, bonds (supramolecular amphiphiles). In this review, we summarize the developments made on the design and synthesis of p-sulfonatocalixarenes-based surfactants, the characterization of their self-assembly properties and on how their structure affects these properties.

INTRODUCTION: Advances achieved over the last few years in drug delivery have provided novel and versatile possibilities for the treatment of various diseases. Among the biomaterials applied in this field, it is worth highlighting the increasing importance of polyaminoacids and polypeptides. The appealing properties of these polymers are very promising for the design of novel compositions in a variety of drug delivery applications. AREAS COVERED: This review provides an overview on the general characteristics of polyaminoacids and polypeptides and briefly discusses different synthetic pathways for their production. This is followed by a detailed description of different drug delivery applications of these polymers, emphasizing those examples that already reached advanced preclinical development or have entered clinical trials. EXPERT OPINION: Polyaminoacids and polypeptides are gaining much attention in drug delivery due to their exceptional properties. Their application as polymers for drug delivery purposes has been sped up by the significant achievements related to their synthesis. Certainly, cancer therapy has benefited the most from these advances, although other fields such as vaccine delivery and alternative administration routes are also being successfully explored. The design of new entities based on polyaminoacids and polypeptides and the improved insight gained in drug delivery guarantee exciting findings in the near future.

A novel fully intermolecular gold-catalyzed [2 + 2 + 2] cycloaddition involving an allenamide, an alkene and an aldehyde provides a straightforward entry to tetrahydropyrans.

Cation–π interactions determine the helical sense adopted by a polyphenylacetylene bearing (<italic>R</italic>)-α-methoxy-α-phenylacetamide as a pendant group (poly-<bold>1</bold>).

The self-aggregation of five amphiphilic p-sulfonatocalix[n]arenes bearing alkyl chains at the lower rim was investigated by NMR spectroscopy and electrical conductivity. The critical micelle concentration was determined, and the tendency of this special class of surfactants to self-aggregate in aqueous solution was analyzed as a function of the alkyl chain length and the number of aromatic units in the macrocyclic ring. The structure of the surfactants in the monomeric and micellized states was elucidated by means of (1)H NMR and, in the case of the calix[6]arene derivative, with 2D NMR experiments. While all amphiphilic calix[4]arenes studied here are blocked in the cone conformation, in the monomeric state the calix[6]arene adopts a pseudo-1,2,3-alternate conformation and the calix[8]arene is conformationally mobile. These calixarenes undergo an aggregation-induced conformational change, adopting the cone conformation in the micelles. The structure and size of the aggregates were studied by diffusion ordered spectroscopy (DOSY) experiments, and the results indicate that these surfactants self-assemble into ellipsoidal micelles.

Two regioisomeric series of diaryl 2- or 4-amidopyrimidines have been synthesized and their adenosine receptor affinities were determined in radioligand binding assays at the four human adenosine receptors (hARs). Some of the ligands prepared herein exhibit remarkable affinities (K(i) < 10 nm) and, most noticeably, the absence of activity at the A(1), A(2A), and A(2B) receptors. The structural determinants that support the affinity and selectivity profiles of the series were highlighted through an integrated computational approach, combining a 3D-QSAR model built on the second generation of GRid INdependent Descriptors (GRIND2) with a novel homology model of the hA(3) receptor. The robustness of the computational model was subsequently evaluated by the design of new derivatives exploring the alkyl substituent of the exocyclic amide group. The synthesis and evaluation of the novel compounds validated the predictive power of the model, exhibiting excellent agreement between predicted and experimental activities.

In this work, we have studied the interactions between the water-soluble p-sulfonatocalix[6]arene and cationic surfactants octyltrimethylammonium bromide below the cmc and dodecyltrimethylammonium bromide above the cmc, by saturation transfer difference (STD) NMR spectroscopy. From the STD build-up curves, we have obtained the T1 independent cross relaxation rates, and the results show that the interactions established between the cationic headgroup of the surfactant and the OMe group of the macrocycle play an important role in the stabilization of the complex, both below and above the cmc.

We present a simple procedure for the synthesis of quasi-spherical Au nanoparticles in a wide size range mediated by macrocyclic host molecules, ammonium pillar[5]arene (AP[5]A). The strategy is based on a seeded growth process in which the water-soluble pillar[5]arene undergoes complexation of the Au salt through the ammonium groups, thereby avoiding Au nucleation, while acting as a stabilizer. The presence of the pillar[5]arene onto the Au nanoparticle particle surface is demonstrated by surface-enhanced Raman scattering (SERS) spectroscopy, and the most probable conformation of the molecule when adsorbed on the Au nanoparticles surface is suggested on the basis of theoretical calculations. In addition, we analyze the host-guest interactions of the AP[5]A with 2-naphthoic acid (2NA) by using (1)H NMR spectroscopy and the results are compared with theoretical calculations. Finally, the promising synergetic effects of combining supramolecular chemistry and metal nanoparticles are demonstrated through SERS detection in water of 2NA and a polycyclic aromatic hydrocarbon, pyrene (PYR).

A microcalorimetric study on the inclusion of monovalent and divalent metal cations by p-sulfonatocalix[4]arene was performed. The thermodynamic parameters for the complexation of alkali metal cations and Ag(+) were obtained for the first time at neutral pH. The Na(+) cation is routinely present as counterion of the calixarene in neutral aqueous solution, and this must be taken into account in the determination of the thermodynamic parameters for the complexation of Na(+) and the other cations by considering a sequential or a competitive binding scheme. The ΔH° and ΔS° values show that the inclusion process is entropically driven, although an influence of the temperature on the complexation reaction indicates that the enthalpic term is also an important contributor. The results also reveal that enthalpy/entropy compensation balances the gain in one contribution against a corresponding loss in the other. The obtained thermodynamic data are in contrast to the results from previous microcalorimetric studies, which showed binding constants that were orders of magnitude smaller and complexations, which were in part enthalpically driven but which neglected the influence of the alkali metal counterions.

This work presents an accurate way for calculating partition functions of strongly coupled hindered rotors in two dimensions. The two-dimensional torsional potential is generated from electronic structure calculations and fitted to Fourier series. The kinetic energy includes off-diagonal terms which are allowed to vary with the torsional angles, and these terms were also fitted to Fourier series. The resulting Hamiltonian leads to a coupled Schrödinger equation which was solved by the variational method. Therefore, the final two-dimensional non-separable (2D-NS) partition function incorporates coupling terms in both the kinetic and the potential energy. The methodology has been tested for propane, methyl formate, and a hydrogen abstraction transition state from propanone by the OH radical. How to incorporate the 2D-NS partition function in the total vibrational-rotational partition function is also discussed.

The potential energy surface of protonated uracil has been explored by an automated transition state search procedure, resulting in the finding of 1398 stationary points and 751 reactive channels, which can be categorized into isomerizations between pairs of isomers, unimolecular fragmentations and bimolecular reactions. The use of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory and Kinetic Monte Carlo (KMC) simulations allowed us to determine the relative abundances of each fragmentation channel as a function of the ion's internal energy. The KMC/RRKM product abundances are compared with novel mass spectrometry (MS) experiments in the collision energy range 1-6 eV. To facilitate the comparison between theory and experiments, further dynamics simulations are carried out to determine the fraction of collision energy converted into the ion's internal energy. The KMC simulations show that the major fragmentation channels are isocyanic acid and ammonia losses, in good agreement with experiments. The third predominant channel is water loss according to both theory and experiments, although the abundance obtained in the KMC simulations is very low, suggesting that non-statistical dynamics might play an important role in this channel. Isocyanic acid (HNCOH(+)) is also an important product in the KMC simulations, although its abundance is only significant at internal energies not accessible in the MS experiments.

amide conformation at the pendant groups allows the controlled formation and cleavage of the stereocomplex due to a dramatic change between the intermolecular and intramolecular hydrogen bond interactions.

Novel plasmonic thin films based on electrostatic layer-by-layer (LbL) deposition of citrate-stabilized Au nanoparticles (NPs) and ammonium pillar[5]arene (AP[5]A) have been developed. The supramolecular-induced LbL assembly of the plasmonic nanoparticles yields the formation of controlled hot spots with uniform interparticle distances. At the same time, this strategy allows modulating the density and dimensions of the Au aggregates, and therefore the optical response, on the thin film with the number of AuNP-AP[5]A deposition cycles. Characterization of the AuNP-AP[5]A hybrid platforms as a function of the deposition cycles was performed by means of visible–NIR absorption spectroscopy, and scanning electron and atomic force microscopies, showing larger aggregates with the number of cycles. Additionally, the surface enhanced Raman scattering efficiency of the resulting AuNP-AP[5]A thin films has been investigated for three different laser excitations (633, 785, and 830 nm) and using pyrene as Raman probe. The best performance was shown by the AuNP-AP[5]A film obtained with two deposition cycles ((AuNP-AP[5]A)2) when excited with a 785 laser line. The optical response and SERS efficiency of the thin films were also simulated using the M3 solver and employing computer aided design models built based on SEM images of the different films. The use of host molecules as building blocks to fabricate (AuNP-AP[5]A)2) films has enabled the ultradetection, in liquid and gas phase, of low molecular weight polyaromatic hydrocarbons, PAHs, with no affinity for gold but toward the hydrophobic AP[5]A cavity. Besides, these plasmonic platforms allowed achieving quantitative detection within certain concentration regimes. Finally, the multiplex sensing capabilities of the AuNP-AP[5]A)2 were evaluated for their ability to detect in liquid and gas phase three different PAHs.

Aldehydes can be α-alkylated with allenamides by the combined action of an organocatalyst and a gold complex. The reaction requires the simultaneous generation of an enamine and a gold-activated allenamide. Importantly, by using a chiral amine as organocatalyst it is possible to obtain aldehyde products featuring all-carbon quaternary stereocenter at their α-position, with moderate to good levels of enantioselectivity.

Thermodynamic parameters obtained from studying the micellization of amphiphilic p-sulfonatocalix[n]arenes were correlated with the alkyl chain length and with the number of monomeric units (n) in the calix[n]arene structure. The micellization Gibbs free energy (ΔG(M)(o)) becomes more negative upon increasing the alkyl chain length of the p-sulfonatocalix[4]arene. This is in agreement with the trend generally observed for other surfactants. However, the ΔG(M)(o) value for transferring one CH(2) group from the bulk aqueous medium to the micelle [ΔG(M)(o)(CH(2))] is lower than the value generally observed for single-chain surfactants, suggesting the existence of intramolecular interactions between the alkyl chains of the free unimers. On the other hand, the critical micelle concentration (cmc; per alkyl chain unit) increased with the increasing number of monomeric units. These results are explained on the basis of the conformation adopted by the calixarene in the bulk solution. The calix[4]arene derivatives are preorganized into the cone conformation, which is favorable for the formation of globular aggregates. The calix[6]arene and calix[8]arene derivatives do not adopt cone conformations. Changing these conformations to the more favorable cone conformer in the aggregates implies an energetic cost that contributes to making ΔG(M)(o) less efficient. In the case of the calix[6]arene derivative this energetic cost is enthalpic, whereas in the case of the octamer it is both enthalpic and entropic. Both the ΔG(M)(o)(CH(2)) value and the change in heat capacity (ΔCp(M)(o)) seem to indicate that for the cone calix[4]arene derivatives all alkyl chains are solvated by the same hydration shell, whereas in the case of the highly flexible calix[8]arene derivative each alkyl chain is individually hydrated.