Interaction between glyphosate pesticide and amphiphilic peptides for colorimetric analysis.

The large-scale use of glyphosate pesticides in food production has attracted attention due to environmental damage and toxicity risks. Several regulatory authorities have established safe limits or concentrations of these pesticides in water and various food products consumed daily. The irreversible inhibition of acetylcholinesterase (AChE) activity is one of the strategies used for pesticide detection. Herein, we found that lipopeptide sequences can act as biomimetic microenvironments of AChE, showing higher catalytic activities than natural enzymes in an aqueous solution, based on IC50 values. These biomolecules contain in the hydrophilic part the amino acids l-proline (P), l-arginine (R), l-tryptophan (W), and l-glycine (G), covalently linked to a hydrophobic part formed by one or two long aliphatic chains. The obtained materials are referred to as compounds 1 and 2, respectively. According to fluorescence assays, 2 is more hydrophobic than 1. The circular dichroism (CD) data present a significant difference in the molar ellipticity values, likely related to distinct conformations assumed by the proline residue in the lipopeptide supramolecular structure in solution. The morphological aspect was further characterized using small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM), which showed that compounds 1 and 2 self-assembly into cylindrical and planar core-shell structures, respectively. The mimetic AchE behaviour of lipopeptides was confirmed by Ellman's hydrolysis reaction, where the proline residue in the peptides act as a nucleophilic scavenger of organophosphate pesticides. Moreover, the isothermal titration calorimetry (ITC) experiments revealed that host-guest interactions in both systems were dominated by enthalpically-driven thermodynamics. UV-vis kinetic experiments were performed to assess the inhibition of the lipopeptide catalytic activity and the IC50 values were obtained, and we found that the detection limit correlated with the increase in hydrophobicity of the lipopeptides, implying the micellization process is more favorable.

Structure optimization of lipopeptide assemblies for aldol reactions in an aqueous medium.

Four amphiphilic peptides were synthesized, characterized, and evaluated regarding their efficiency in the catalysis of direct aldol reactions in water. The lipopeptides differ by having a double lipid chain and a guanidinium pyrrole group functionalizing one Lys side chain. All the samples are composed of the amino acids l-proline (P), l-arginine (R), or l-lysine (K) functionalized with the cationic guanidiniocarbonyl pyrrole unit (GCP), l-tryptophan (W), and l-glycine (G), covalently linked to one or two long aliphatic chains, leading to surfactant-like designs with controlled proline protonation state and different stereoselectivity. Critical aggregation concentrations (cac) were higher in the presence of the GCP group, suggesting that self-assembly depends on charge distribution along the peptide backbone. Cryogenic Transmission Electron Microscopy (Cryo-TEM) and Small Angle X-ray Scattering (SAXS) showed a rich polymorphism including spherical, cylindrical, and bilayer structures. Molecular dynamics simulations performed to assess the lipopeptide polymorphs revealed an excellent agreement with core-shell arrangements derived from SAXS data and provided an atomistic view of the changes incurred by modifying head groups and lipid chains. The resulting nanostructures behaved as excellent catalysts for aldol condensation reactions, in which superior conversions (>99%), high diastereoselectivities (ds = 94 : 6), and enantioselectivities (ee = 92%) were obtained. Our findings contribute to elucidate the effect of nanoscale organization of lipopeptide assemblies in the catalysis of aldol reactions in an aqueous environment.

First principles theoretical spectroscopy of methylene blue: Between limitations of time-dependent density functional theory approximations and its realistic description in the solvent.

Methylene blue [3,7-Bis(di-methylamino) phenothiazin-5-ium chloride] is a phenothiazine dye with applications as a sensitizer for photodynamic therapy, photoantimicrobials, and dye-sensitized solar cells. Time-dependent density functional theory (TDDFT), based on (semi)local and global hybrid exchange-correlation functionals, fails to correctly describe its spectral features due to known limitations for describing optical excitations of π-conjugated systems. Here, we use TDDFT with a non-empirical optimally tuned range-separated hybrid functional to explore the optical excitations of gas phase and solvated methylene blue. We compute solvated configurations using molecular dynamics and an iterative procedure to account for explicit solute polarization. We rationalize and validate that by extrapolating the optimized range separation parameter to an infinite amount of solvating molecules, the optical gap of methylene blue is well described. Moreover, this method allows us to resolve contributions from solvent-solute intermolecular interactions and dielectric screening. We validate our results by comparing them to first-principles calculations based on the GW+Bethe-Salpeter equation approach and experiment. Vibronic calculations using TDDFT and the generating function method account for the spectra's subbands and bring the computed transition energies to within 0.15 eV of the experimental data. This methodology is expected to perform equivalently well for describing solvated spectra of π-conjugated systems.

Density Functional Theory Applied to Excited State Intramolecular Proton Transfer in Imidazole-, Oxazole-, and Thiazole-Based Systems.

Excited state intramolecular proton transfer (ESIPT) is a photoinduced process strongly associated to hydrogen bonding within a molecular framework. In this manuscript, we computed potential energy data using Time Dependent Density Functional Theory (TDDFT) for triphenyl-substituted heterocycles, which evidenced an energetically favorable proton transfer on the excited state (i.e., ESIPT) but not on the ground state. Moreover, we describe how changes on heterocyclic functionalities, based on imidazole, oxazole, and thiazole systems, affect the ESIPT process that converts an enolic species to a ketonic one through photon-induced proton transfer. Structural and photophysical data were obtained theoretically by means of density functional theory (DFT) calculations and contrasted for the three heterocyclics. Different functionals were used, but B3LYP was the one that adequately predicted absorption data. It was observed that the intramolecular hydrogen bond is strengthened in the excited state, supporting the occurrence of ESIPT. Finally, it was observed that, with the formation of the excited state, there is a decrease in electronic density at the oxygen atom that acts as proton donor, while there is a substantial increase in the corresponding density at the nitrogen atom that serves as proton acceptor, thus, indicating that proton transfer is indeed favored after photon absorption.

Morphological dependence of silver electrodeposits investigated by changing the ionic liquid solvent and the deposition parameters.

The low toxicity and environmentally compatible ionic liquids (ILs) are alternatives to the toxic and harmful cyanide-based baths used in industrial silver electrodeposition. Here, we report the successful galvanostatic electrodeposition of silver films using the air and water stable ILs 1-ethyl-3-methylimidazolium trifluoromethylsulfonate ([EMIM]TfO) and 1-H-3-methylimidazolium hydrogen sulphate ([HMIM(+)][HSO4(-)]) as solvents and AgTfO as the source of silver. The electrochemical deposition parameters were thoughtfully studied by cyclic voltammetry before deposition. The electrodeposits were characterized by scanning electron microscopy coupled with X-ray energy dispersive spectroscopy and X-ray diffraction. Molecular dynamics (MD) simulations were used to investigate the structural dynamic and energetic properties of AgTfO in both ILs. Cyclic voltammetry experiments revealed that the reduction of silver is a diffusion-controlled process. The morphology of the silver coatings obtained in [EMIM]TfO is independent of the applied current density, resulting in nodular electrodeposits grouped as crystalline clusters. However, the current density significantly influences the morphology of silver electrodeposits obtained in [HMIM(+)][HSO4(-)], thus evolving from dendrites at 15 mA cm(-2) to the coexistence of dendrites and columnar shapes at 30 mA cm(-2). These differences are probably due to the greater interaction of Ag(+) with [HSO4(-)] than with TfO(-), as indicated by the MD simulations. The morphology of Ag deposits is independent of the electrodeposition temperature for both ILs, but higher values of temperature promoted increased cluster sizes. Pure face-centred cubic polycrystalline Ag was deposited on the films with crystallite sizes on the nanometre scale. The morphological dependence of Ag electrodeposits obtained in the [HMIM(+)][HSO4(-)] IL on the current density applied opens up the opportunity to produce different and predetermined Ag deposits.

Urea enhances the photodynamic efficiency of methylene blue.

Methylene blue (MB) is a well-known photosensitizer used mostly for antimicrobial photodynamic therapy (APDT). MB tends to aggregate, interfering negatively with its singlet oxygen generation, because MB aggregates lean towards electron transfer reactions, instead of energy transfer with oxygen. In order to avoid MB aggregation we tested the effect of urea, which destabilizes solute-solute interactions. The antimicrobial efficiency of MB (30 µM) either in water or in 2M aqueous urea solution was tested against a fungus (Candida albicans). Samples were kept in the dark and irradiation was performed with a light emitting diode (λ = 645 nm). Without urea, 9 min of irradiation was needed to achieve complete microbial eradication. In urea solution, complete eradication was obtained with 6 min illumination (light energy of 14.4 J). The higher efficiency of MB/urea solution was correlated with a smaller concentration of dimers, even in the presence of the microorganisms. Monomer to dimer concentration ratios were extracted from the absorption spectra of MB solutions measured as a function of MB concentration at different temperatures and at different concentrations of sodium chloride and urea. Dimerization equilibrium decreased by 3 and 6 times in 1 and 2M urea, respectively, and increased by a factor of 6 in 1M sodium chloride. The destabilization of aggregates by urea seems to be applied to other photosensitizers, since urea also destabilized aggregation of Meso-tetra(4-n-methyl-pyridyl)porphyrin, which is a positively charged porphyrin. We showed that urea destabilizes MB aggregates mainly by causing a decrease in the enthalpic gain of dimerization, which was exactly the opposite of the effect of sodium chloride. In order to understand this phenomenon at the molecular level, we computed the free energy for the dimer association process (ΔG(dimer)) in aqueous solution as well as its enthalpic component in aqueous and in aqueous/urea solutions by molecular dynamics simulations. In 2M-urea solution the atomistic picture revealed a preferential solvation of MB by urea compared with MB dimers while changes in ΔH(dimer) values demonstrated a clear shift favoring MB monomers. Therefore, MB monomers are more stable in urea solutions, which have significantly better photophysics and higher antimicrobial activity. This information can be of use for dental and medical professionals that are using MB based APDT protocols.

Self-assembly of Arg-Phe nanostructures via the solid-vapor phase method.

We report for the first time on the self-assembly of nanostructures composed exclusively of alternating positively charged and hydrophobic amino acids. A novel arginine/phenylalanine octapeptide, RF8, was synthesized. Because the low hydrophobicity of this sequence makes its spontaneous ordering through solution-based methods difficult, a recently proposed solid-vapor approach was used to obtain nanometric architectures on ITO/PET substrates. The formation of the nanostructures was investigated under different preparation conditions, specifically, under different gas-phase solvents (aniline, water, and dichloromethane), different peptide concentrations in the precursor solution, and different incubation times. The stability of the assemblies was experimentally studied by electron microscopy and thermogravimetric analysis coupled with mass spectrometry. The secondary structure was assessed by infrared and Raman spectroscopy, and the arrays were found to assume an antiparallel ß-sheet conformation. FEG-SEM images clearly reveal the appearance of fibrillar structures that form extensive homogeneously distributed networks. A close relationship between the morphology and preparation parameters was found, and a concentration-triggered mechanism was suggested. Molecular dynamics simulations were performed to address the thermal stability and nature of intermolecular interactions of the putative assembly structure. Results obtained when water is considered as solvent shows that a stable lamellar structure is formed containing a thin layer of water in between the RF8 peptides that is stabilized by H-bonding.

Multiconfigurational time-dependent Hartree calculations for tunneling splittings of vibrational states: Theoretical considerations and application to malonaldehyde.

Full-dimensional multiconfigurational time-dependent Hartree calculations on the tunneling splitting of the vibrational ground state and the low lying excited states of malonaldehyde are presented. Methodological developments utilizing the symmetry of double well systems for the efficient calculation of tunneling splittings are described and discussed. Important aspects of the theory underlying the previously communicated results for the ground state tunneling splitting [M. D. Coutinho-Neto et al., J. Chem. Phys. 121, 9207 (2004)] are detailed and further developments facilitating the calculation of tunneling splittings for vibrationally excited states are introduced. Utilizing these developments, the 14 lowest vibrational states of malonaldehyde, i.e., seven tunneling splittings, have been computed. The tunneling splittings are found to vary significantly depending on the particular vibrational excitation. This results in a complex pattern of vibrational levels. Studying the dependence of the tunneling splittings on the vibrational excitation, good agreement with available experimental results is found and intuitive interpretations of the results can be given.

Importance of van der Waals interactions in liquid water.

We present ab initio molecular dynamics studies on liquid water using density functional theory in conjunction with either dispersion-corrected atom-centered potentials or empirical van der Waals corrections. Our results show that improving the description of van der Waals interactions in DFT-GGA leads to a softening of liquid water's structure with higher mobility. The results obtained with dispersion-corrected atom-centered potentials are especially encouraging. In particular, the radial distribution functions are in better agreement with experiment, and the self-diffusion coefficient increases by more than three-fold compared with the one predicted by the BLYP functional. This work demonstrates that van der Waals interactions are essential in fine-tuning both structural and dynamical properties of liquid water.

Predicting noncovalent interactions between aromatic biomolecules with London-dispersion-corrected DFT.

Within the framework of Kohn-Sham density functional theory, interaction energies of hydrogen bonded and pi-pi stacked supramolecular complexes of aromatic heterocycles, nucleobase pairs, and complexes of nucleobases with the anti-cancer agent ellipticine as well as its derivatives are evaluated. Dispersion-corrected atom-centered potentials (DCACPs) are employed together with a generalized gradient approximation to the exchange correlation functional. For all systems presented, the DCACP calculations are in very good agreement with available post Hartree-Fock quantum chemical results. Estimates of 3-body contributions (<15% of the respective interaction energy) and deformation energies (5-15% of the interaction energy) are given. Based on our results, we predict a strongly bound interaction energy profile for the ellipticine intercalation process with a stabilization of nearly 40 kcal/mol (deformation energy not taken into account) when fully intercalated. The frontier orbitals of the intercalator-nucleobase complex and the corresponding non-intercalated nucleobases are investigated and show significant changes upon intercalation. The results not only offer some insights into the systems investigated but also suggest that DCACPs can serve as an effective way to achieve higher accuracy in density functional theory without incurring an unaffordable computational overhead, paving ways for more realistic studies on biomolecular complexes in the condensed phase.

The ground state tunneling splitting and the zero point energy of malonaldehyde: a quantum Monte Carlo determination.

Quantum dynamics calculations of the ground state tunneling splitting and of the zero point energy of malonaldehyde on the full dimensional potential energy surface proposed by Yagi et al. [J. Chem. Phys. 1154, 10647 (2001)] are reported. The exact diffusion Monte Carlo and the projection operator imaginary time spectral evolution methods are used to compute accurate benchmark results for this 21-dimensional ab initio potential energy surface. A tunneling splitting of 25.7+/-0.3 cm-1 is obtained, and the vibrational ground state energy is found to be 15 122+/-4 cm-1. Isotopic substitution of the tunneling hydrogen modifies the tunneling splitting down to 3.21+/-0.09 cm-1 and the vibrational ground state energy to 14 385+/-2 cm-1. The computed tunneling splittings are slightly higher than the experimental values as expected from the potential energy surface which slightly underestimates the barrier height, and they are slightly lower than the results from the instanton theory obtained using the same potential energy surface.

Weakly Bonded Complexes of Aliphatic and Aromatic Carbon Compounds Described with Dispersion Corrected Density Functional Theory.

Interaction energies and structural properties of van der Waals complexes of aliphatic hydrocarbons molecules and crystals of aromatic hydrocarbon compounds are studied using density functional theory augmented with dispersion corrected atom centered potentials (DCACPs). We compare the performance of two sets of DCACPs, (a) DCACP-MP2, a correction for carbon only, generated using MP2 reference data and a penalty functional that includes only equilibrium properties and (b) DCACP-CCSD(T), a set that has been calibrated against CCSD(T) reference data using a more elaborate penalty functional that explicitly takes into account some long-range properties and uses DCACP corrections for hydrogen and carbon atoms. The agreement between our results and high level ab initio or experimental data illustrates the transferability of the DCACP scheme for the gas and condensed phase as well as for different hybridization states of carbon. The typical error of binding energies for gas-phase dimers amounts to 0.3 kcal/mol. This work demonstrates that only one DCACP per element is sufficient to correct for weak interactions in a large variety of systems, irrespective of the hybridization state.

The ground state tunneling splitting of malonaldehyde: accurate full dimensional quantum dynamics calculations.

Benchmark calculations of the tunneling splitting in malonaldehyde using the full dimensional potential proposed by Yagi et al. are reported. Two exact quantum dynamics methods are used: the multiconfigurational time-dependent Hartree (MCTDH) approach and the diffusion Monte Carlo based projection operator imaginary time spectral evolution (POITSE) method. A ground state tunneling splitting of 25.7+/-0.3 cm(-1) is calculated using POITSE. The MCTDH computation yields 25 cm(-1) converged to about 10% accuracy. These rigorous results are used to evaluate the accuracy of approximate dynamical approaches, e.g., the instanton theory.