Ignacio Pérez-Juste

Detection and imaging of quorum sensing in Pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering

Most bacteria in nature exist as biofilms, which support intercellular signaling processes such as quorum sensing (QS), a cell-to-cell communication mechanism that allows bacteria to monitor and respond to cell density and changes in the environment. Because QS and biofilms are involved in the ability of bacteria to cause disease, there is a need for the development of methods for the non-invasive analysis of QS in natural bacterial populations. Here, by using surface-enhanced resonance Raman scattering spectroscopy, we report rationally designed nanostructured plasmonic substrates for the in-situ, label-free detection of a QS signaling metabolite in growing Pseudomonas aeruginosa biofilms and microcolonies. The in situ, non-invasive plasmonic imaging of QS in biofilms provides a powerful analytical approach for studying intercellular communication on the basis of secreted molecules as signals.

INFLUENCE OF CALCULATION LEVEL AND EFFECT OF METHYLATION ON AXIAL/EQUATORIAL EQUILIBRIA IN PIPERIDINES

A detailed conformational analysis was performed on the chair forms of piperidine, N‐methylpiperidine, and some methylated derivatives using Hartree–Fock (HF) and MP2 ab initio methods with several basis sets (from 3–21G to 6–311++G**), and the most widely used semiempirical approaches (MNDO, AM1, and PM3). It was found that the use of polarized basis sets at the HF level is adequate enough for the prediction of conformational preferences in the axial/equatorial equilibrium of the N‐R group in piperidines. On the other hand, the inclusion of electron correlation becomes necessary for predicting the axial/equatorial energy differences of the equilibria of the methyl group. Semiempirical methods are not recommended, because AM1 and PM3 predict opposite stabilities to those obtained experimentally and MNDO ring geometries are systematically too flat. The origin of the conformational stabilities was interpreted in terms of the natural bond orbital analysis of the HF/6–31G** wave functions. The equatorial preferences in the N‐H equilibria is mainly due to lower Lewis energies, although delocalization of the nitrogen lone pair is favored in N‐H axial forms. N‐Methylation increases the equatorial M‐Me preferences, because the Lewis energy of axial N‐Me forms increases due to larger 1,3‐diaxial interactions. Geometrical trends associated with the delocalization of the nitrogen lone pair and with interactions between the introduced N‐R and C‐Me groups were discussed and related to the degree of planarity of the six‐membered ring by means of the puckering coordinates defined by Pople and Cremer. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 961–976, 1998

Aromaticity in spin-polarized systems: Can rings be simultaneously alpha aromatic and beta antiaromatic?

The partition of the multicenter electron delocalization indices and the nucleus independent chemical shift indices into alpha and beta contributions in open-shell systems has been performed. In general it is shown that a full understanding of aromaticity in these systems cannot be achieved by restricting the calculations to the global properties but by dissecting these properties into alpha and beta terms. The 4n+2- and 4n-aromaticity rules for singlet and triplet annulenes, respectively, reduce to a general aromaticity rule when the alpha and beta terms are studied separately. This new rule allows us to extend the concept of conflicting aromaticities to radical systems that are simultaneously alpha-aromatic and beta-antiaromatic or vice versa. The existence of such systems is demonstrated here by means of multicenter electron delocalization indices and nucleus independent chemical shifts. Finally, the global aromatic/antiaromatic character of these radical systems is estimated by means of aromatic stabilization energy, which is shown to be either slightly positive or slightly negative, thus reflecting the small aromatic/antiaromatic character of these radicals and reinforcing the conclusions obtained with aromaticity indices.

Pillar[5]arene‐Mediated Synthesis of Gold Nanoparticles: Size Control and Sensing Capabilities

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).

Theoretical study of the electronic structure of CnS (n=1–6) thiocumulenes

Linear sulfur-carbon chains C(n)S (n=1-6) of astronomical interest were examined by means of several theoretical methods. The three smallest compounds of the series were chosen to evaluate the performance of several computational models, including Hartree-Fock theory, density functional theory with the Beckes three parameter exchange functional and the correlation functional of Lee, Yang, and Parr (B3LYP), and electron-correlated methods (second-order Moller-Plesset perturbation method (MP2), configuration interaction method including single and double excitations (CISD), and quadratic configuration interaction method including single and double excitations (QCISD) in combination with a large variety of basis sets. The systematic comparison between the experiment and theory indicates that the B3LYP/6-311G** method can be considered suitable for the study of the electronic structures of the C(n)S compounds. The electronic ground states of the C(n)S molecules alternate between 1Sigma and 3Sigma for odd and even values of n, respectively. The B3LYP/6-311G** wave functions for these electronic ground states were analyzed by means of the atoms in molecules (AIM) and natural bond orbital (NBO) methods. Both approaches suggest that the electronic structures for the singlet and triplet compounds must be considered separately. According to the NBO method, singlet compounds can be properly represented by acetylenic structures with alternating single and triple bonds (S[triple bond]C-C[triple bond]C...). However, triplet compounds are better described by means of double bond-double bond cumulenic structures (S=C=C=C=C...) as a consequence of the average between different alpha and beta electronic densities. AIM delocalization indexes and NBO interactions between localized orbitals also indicate that these structures are strongly pi delocalized. Finally, the different singlet and triplet structures proposed provide a consistent explanation for the geometries, dipole moments, and spin-density values of the C(n)S compounds studied.

INFLUENCE OF WATER IN THE TAUTOMERISM OF 2,2'-BIPYRIDINE-3,3'-DIOL

Abstract Excited-state proton transfer processes (ESPT) have been widely studied in recent years. Two protons can be transferred via an ESPT process in [2,2′-bipyridine]-3,3′-diol (BPD). Experimental studies have been carried out to explain the spectroscopic behaviour and its relationship with tautomerization. For analogous species, it has been established that the solvent may participate in the interconversion mechanism or that it may influence the relative stabilities of the tautomeric species. We have studied, with ab initio and semiempirical methods, the influence of water in the tautomerization process. We have found that water stabilizes both tautomeric forms in a different amount. This effect is not observed in other polar or non-polar solvents. Additionally, it has been found that discrete interactions of two water molecules on each side of the molecule are needed for predicting this behaviour.

Encapsulation of Single Plasmonic Nanoparticles within ZIF-8 and SERS Analysis of the MOF Flexibility

Hybrid nanostructures composed of metal nanoparticles and metal-organic frameworks (MOFs) have recently received increasing attention toward various applications due to the combination of optical and catalytic properties of nanometals with the large internal surface area, tunable crystal porosity and unique chemical properties of MOFs. Encapsulation of metal nanoparticles of well-defined shapes into porous MOFs in a core-shell type configuration can thus lead to enhanced stability and selectivity in applications such as sensing or catalysis. In this study, the encapsulation of single noble metal nanoparticles with arbitrary shapes within zeolitic imidazolate-based metal organic frameworks (ZIF-8) is demonstrated. The synthetic strategy is based on the enhanced interaction between ZIF-8 nanocrystals and metal nanoparticle surfaces covered by quaternary ammonium surfactants. High resolution electron microscopy and tomography confirm a complete core-shell morphology. Such a well-defined morphology allowed us to study the transport of guest molecules through the ZIF-8 porous shell by means of surface-enhanced Raman scattering by the metal cores. The results demonstrate that even molecules larger than the ZIF-8 aperture and pore size may be able to diffuse through the framework and reach the metal core.

A β-cyclodextrin–resveratrol inclusion complex and the role of geometrical and electronic effects on its electronic induced circular dichroism

Complexation of trans-resveratrol with β-cyclodextrin results in an induced Cotton effect (ICD). On the basis of NMR T-ROESY experiments and molecular dynamics simulations a preferential orientation mode of resveratrol within the cyclodextrin is proposed, in which the dihydroxyl ring is oriented towards the narrow side of the β-cyclodextrin. TD-DFT calculations showed that the observed ICD is caused by orbital mixing on trans-resveratrol upon complexation with β-cyclodextrin, being geometry effects averaged out by the flexibility of resveratrol inside the CD cavity. Computations also show that Harata–Kodaka rules are not of direct applicability to systems like resveratrol where the chromophore is only partially buried into the cyclodextrin cavity.

Imaging Bacterial Interspecies Chemical Interactions by Surface-Enhanced Raman Scattering

Microbes produce bioactive chemical compounds to influence the physiology and growth of their neighbors, and our understanding of their biological activities may be enhanced by our ability to visualize such molecules in vivo. We demonstrate here the application of surface-enhanced Raman scattering spectroscopy for simultaneous detection of quorum-sensing-regulated pyocyanin and violacein, produced respectively by Pseudomonas aeruginosa and Chromobacterium violaceum bacterial colonies, grown as a coculture on agar-based plasmonic substrates. Our plasmonic approach allowed us to visualize the expression and spatial distribution of the microbial metabolites in the coculture taking place as a result of interspecies chemical interactions. By combining surface-enhanced Raman scattering spectroscopy with analysis of gene expression we provide insight into the chemical interplay occurring between the interacting bacterial species. This highly sensitive, cost-effective, and easy to implement approach allows spatiotemporal imaging of cellular metabolites in live microbial colonies grown on agar with no need for sample preparation, thereby providing a powerful tool for the analysis of microbial chemotypes.

Theoretical study of the electronic structure of HXY/XYH radicals (XC,Si;YO,S)

The electronic structures of the HXY/XYH compounds (XC,Si;YO,S) on the A′2 electronic ground state were investigated by applying the natural bond orbital (NBO) method to the computed B3LYP∕6-311G** wave functions. Different localized structures are proposed for the HXY and XYH isomers and the central XY unit is described as intermediate between a double and a triple bond in HCO, HCS, HSiO, and HSiS, similar to a double bond in COH, CSH, and SiSH, and clearly a single bond in SiOH. Through the comparison between the NBO results for the diatomic and hydrogenated compounds, the energy preferences on each pair of isomers and the computed geometrical parameters are explained. According to the structures proposed, the HXY compounds are σ radicals with the spin density distributed along the molecular framework, while the XYH compounds are π radicals with most of the unpaired spin located on an almost pure p orbital of the X atom. Finally, the amounts of spin density on natural atomic orbitals provided by the N...