Interface-Dependent Selectivity in Plasmon-Driven Chemical Reactions.

Plasmonic nanoparticles can drive chemical reactions powered by sunlight. These processes involve the excitation of surface plasmon resonances (SPR) and the subsequent charge transfer to adsorbed molecular orbitals. Nonetheless, controlling the flow of energy and charge from SPR to adsorbed molecules is still difficult to predict or tune. Here, we show the crucial role of halide ions in modifying the energy landscape of a plasmon-driven chemical reaction by carefully engineering the nanoparticle-molecule interface. By doing so, the selectivity of plasmon-driven chemical reactions can be controlled, either enhancing or inhibiting the metal-molecule charge and energy transfer or by regulating the vibrational pumping rate. These results provide an elegant method for controlling the energy flow from plasmonic nanoparticles to adsorbed molecules, in situ, and selectively targeting chemical bonds by changing the chemical nature of the metal-molecule interface.

All-Atom Molecular Dynamics Investigations on the Interactions between D2 Subunit Dopamine Receptors and Three 11C-Labeled Radiopharmaceutical Ligands.

The D2 subunit dopamine receptor represents a key factor in modulating dopamine release. Moreover, the investigated radiopharmaceutical ligands used in positron emission tomography imaging techniques are known to bind D2 receptors, allowing for dopaminergic pathways quantification in the living human brain. Thus, the biophysical characterization of these radioligands is expected to provide additional insights into the interaction mechanisms between the vehicle molecules and their targets. Using molecular dynamics simulations and QM calculations, the present study aimed to investigate the potential positions in which the D2 dopamine receptor would most likely interact with the three distinctive synthetic 11C-labeled compounds (raclopride (3,5-dichloro-N-[[(2S)-1-ethylpyrrolidin-2-yl]methyl]-2-hydroxy-6-methoxybenzamide)-RACL, FLB457 (5-bromo-N-[[(2S)-1-ethylpyrrolidin-2-yl]methyl]-2,3-dimethoxybenzamide)-FLB457 and SCH23390 (R(+)-7-Chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine)-SCH)), as well as to estimate the binding affinities of the ligand-receptor complexes. A docking study was performed prior to multiple 50 ns molecular dynamics productions for the ligands situated at the top and bottom interacting pockets of the receptor. The most prominent motions for the RACL ligand were described by the high fluctuations of the peripheral aliphatic -CH3 groups and by its C-Cl aromatic ring groups. In good agreement with the experimental data, the D2 dopamine receptor-RACL complex showed the highest interacting patterns for ligands docked at the receptor's top position.

Decreased Interactions between Calmodulin and a Mutant Huntingtin Model Might Reduce the Cytotoxic Level of Intracellular Ca2+: A Molecular Dynamics Study.

Mutant huntingtin (m-HTT) proteins and calmodulin (CaM) co-localize in the cerebral cortex with significant effects on the intracellular calcium levels by altering the specific calcium-mediated signals. Furthermore, the mutant huntingtin proteins show great affinity for CaM that can lead to a further stabilization of the mutant huntingtin aggregates. In this context, the present study focuses on describing the interactions between CaM and two huntingtin mutants from a biophysical point of view, by using classical Molecular Dynamics techniques. The huntingtin models consist of a wild-type structure, one mutant with 45 glutamine residues and the second mutant with nine additional key-point mutations from glutamine residues into proline residues (9P(EM) model). Our docking scores and binding free energy calculations show higher binding affinities of all HTT models for the C-lobe end of the CaM protein. In terms of dynamic evolution, the 9P(EM) model triggered great structural changes into the CaM protein's structure and shows the highest fluctuation rates due to its structural transitions at the helical level from α-helices to turns and random coils. Moreover, our proposed 9P(EM) model suggests much lower interaction energies when compared to the 45Qs-HTT mutant model, this finding being in good agreement with the 9P(EM)'s antagonistic effect hypothesis on highly toxic protein-protein interactions.

Theoretical and Experimental Vibrational Characterization of Biologically Active Nd(III) Complex.

The neodymium(III) complex of orotic acid (HOA) was synthesized and its structure determined by means of analytical and spectral analyses. Detailed vibrational analysis of HOA, sodium salt of HOA, and Nd(III)-OA systems based on both the calculated and experimental spectra confirmed the suggested metal-ligand binding mode. Significant differences in the IR and Raman spectra of the complex were observed as compared to the spectra of the ligand. The calculated vibrational wavenumbers, including IR intensities and Raman scattering activities, for the ligand and its Nd(III) complex were in good agreement with the experimental data. The vibrational analysis performed for the studied species, orotic acid, sodium salt of orotic acid, and its Nd(III) complex helped to explain the vibrational behaviour of the ligand's vibrational modes, sensitive to interaction with Nd(III). In this paper we also report preliminary results about the cytotoxicity of the investigated compounds. The cytotoxic effects of the ligand and its Nd(III) complex were determined using the MTT method on different tumour cell lines. The screening performed revealed that the tested compounds exerted cytotoxic activity upon the evaluated cell lines.

Vibrational and Nuclear Magnetic Resonance Properties of 2,2'-Biquinolines: Experimental and Computational Spectroscopy Study.

Experimental (IR, Raman and NMR) techniques and quantum chemical (DFT) methods have been applied to investigate the vibrational and NMR properties of a new ligand based on 2,2'-biquinoline (bq) functionalized with polar hydrophilic tetraethylene glycol monomethylether (TEG) chains (bq_TEG). Vibrational and NMR spectra of the ligand have been explained based on DFT computational data obtained at B3LYP/6-311+G(d,p) level of theory. For the spectroscopic analysis we started from the parent molecule 2,2'-biquinoline and explained the changes in the spectra of bq_TEG in close relation to the corresponding spectra of bq. Our data point to a trans conformation of bq_TEG in solid state, as wells as in liquid phase. The excellent agreement between the experimental and computed data allowed for a reliable assignment of the vibrational and NMR spectra, both for bq and bq_TEG.

Specific Key-Point Mutations along the Helical Conformation of Huntingtin-Exon 1 Protein Might Have an Antagonistic Effect on the Toxic Helical Content's Formation.

The polyglutamine tract length represents a key regulator for the Huntington's disease toxicity level and its aggregation rates, often being related to helical structural conformations. In this study, we performed all-atom MD simulations on mutant Huntingtin-Exon1 protein with additional mutation spots, aiming to observe the corresponding structural and dynamical changes at the level of the helix. The simulated structures consist of three sets of Q residue mutations into P residues (4P, 7P, and 9P), with each set including different spots of mutations: random along the mutant sequence (R models), at the edges of the helix (E models), as well as at the edges and in the middle of the helix (EM models). At the helical level, our results predict less compactness profiles for a higher number of P mutations (7P and 9P models) with particular mutation spots at the edges and at the edges-middle of the helix. Moreover, the C-alpha atom distances decreased for 7P and 9P models in comparison to 4P models, and the RMSF values show the highest fluctuation rates for 9P models with point mutations at the edges and in the middle of the helix. The secondary structure analysis suggests greater structural transitions from α-helices to bends, turns, and random coils for 7P and 9P models, particularly for point mutations considered at the edges and in the middle of the helical content. The obtained results support our hypothesis that specific key-point mutations along the helical conformation might have an antagonistic effect on the toxic helical content's formation.

Diverse coordination of aroylhydrazones toward iron(III) in solid state and in solution: spectrometric, spectroscopic and computational study.

The coordination properties of N'-(2-hydroxy-3-methoxyphenylmethylidene)-3-pyridinecarbohydrazide (H2L1), N'-(2-hydroxy-4-methoxyphenylmethylidene)-3-pyridinecarbohydrazide (H2L2) and N'-(2-hydroxy-5-methoxyphenylmethylidene)-3-pyridinecarbohydrazide (H2L3) toward Fe(III) ions were studied by computational, spectrometric (MS) and spectroscopic methods (UV-Vis, IR and Raman spectroscopy) in solid state and in solution. Free ligands were present in keto-amine form with intramolecular H-bond. In MeOH:H2O 1:1 system, the 1:1 complexes with Fe(III) were formed, characterized by lgK ≥ 6. The coordination to the metal ion was achieved via oxygen and azomethine nitrogen since the hydrolysis of hydrazone bond was suppressed. Unlike the 1:1 stoichiometry in methanolic solution, the composition of the complexes extracted to chloroform was Fe(L)(HL). The release of three protons upon complexation was determined by independent spectrophotometric measurements. The complexes isolated from MeOH/EtOH solution have also stoichiometry 1:2. However, depending on the position of the methoxy substituent, two types of complexes were formed. In Fe(H2L1)2Cl3 and Fe(H2L3)2Cl3, hydrazones acted as neutral ligands, while in Fe(HL2)2Cl the keto-enol tautomeric interconversion and release of one proton per ligand took place. All complexes were analyzed in gas phase as well, using triple quadrupole, ion trap and H/D exchange for determination of labile hydrogens. Based on the fragmentation pathways, the structural isomers were distinguished.

Molecular Dynamics Simulations Applied to Structural and Dynamical Transitions of the Huntingtin Protein: A Review.

Over the recent years, Huntington's disease (HD) has become widely discussed in the scientific literature especially because at the mutant level there are several contradictions regarding the aggregation mechanism. The specific role of the physiological huntingtin protein remains unknown, due to the lack of characterization of its entire crystallographic structure, making the experimental and theoretical research even harder when taking into consideration its involvement in multiple biological functions and its high affinity for different interacting partners. Different types of models, containing fewer (not more than 35 Qs) polyglutamine residues for the WT structure and above 35 Qs for the mutants, were subjected to classical or advanced MD simulations to establish the proteins' structural stability by evaluating their conformational changes. Outside the polyQ tract, there are two other regions of interest (the N17 domain and the polyP rich domain) considered to be essential for the aggregation kinetics at the mutant level. The polymerization process is considered to be dependent on the polyQ length. As the polyQ tract's dimension increases, the structures present more ß-sheet conformations. Contrarily, it is also considered that the aggregation stability is not necessarily dependent on the number of Qs, while the initial stage of the aggregation seed might play the decisive role. A general assumption regarding the polyP domain is that it might preserve the polyQ structures soluble by acting as an antagonist for ß-sheet formation.

Microsphere packages of carotenoids: intact sea urchin eggs tracked by Raman spectroscopy tools.

Although natural exposure to ambient UV radiation in oligotrophic seawater at small depths can reach the levels responsible for cellular damage, the sea urchin Paracentrotus lividus is frequently in such sites, particularly on the southern Adriatic Sea shore. Spawning their eggs and spending their early life stage in rocky shores at depths of 0.5-2 m are the results of their successful adaptation strategies, although adults may dwell at greater depths. Surprisingly, there is a paucity of reports regarding the carotenoid content in sea urchin eggs. Beyond their important role in photoprotection against high UV exposure, cell division and early development, the content and distribution of carotenoids contribute to the successful survival of sea urchins and also determine the color of their gonads (roe), which is of commercial importance as a delicacy. Herein, for the first time, we have described the carotenoid content and distribution in intact, freshly released eggs of P. lividus species, non-destructively employing resonance Raman spectroscopy and imaging; near-infrared Raman spectroscopy revealed additional molecular carotenoid content. Echinenone and ß-carotene resonance Raman signals were the most intense, and they were identified as the principal carotenoids that are preferentially accumulated in eggs rather than in gonads. Raman imaging in confocal mode revealed the uniform distribution of the carotenoid signal over the whole eggs, while the distribution of proteins appeared spotted. Egg carotenoids generally maintained their identity after 2 months of dry storage, with slight signs of C[double bond, length as m-dash]C bond oxidation. The potential utilization of P. lividus sea urchin eggs as valuable microsphere packages of native carotenoids is discussed.

SERS-based quantification of albuminuria in the normal-to-mildly increased range.

The lack of an accurate point-of-care detection system for microalbuminuria represents an important unmet medical need that contributes to the morbidity and mortality of patients with kidney diseases. In this proof-of-concept study, we used SERS spectroscopy to detect urinary albumin concentrations in the normal-to-mildly increased albuminuria range, a strategy that could be useful for the early diagnosis of renal impairment due to uncontrolled hypertension, cardiovascular disease or diabetes. We analyzed 27 urine samples by SERS, using iodide-modified silver nanoparticles and we could discriminate between groups with high and low albumin concentrations with an overall accuracy of 89%, 93% and 89%, using principal component analysis-linear discriminant analysis and cut-off values of 3, 6 and 10 µg mL-1 for urinary albumin concentrations, respectively. We achieved a detection limit of 3 µg mL-1 for human serum albumin based on the 1002 cm-1 SERS band, attributed to the ring breathing vibration of phenylalanine. Our detection limit is similar to that of the immunoturbidimetric assays and around one order of magnitude below the detection limit of urinary dipsticks used to detect microalbuminuria. We used principal least squares regression for building a spectral model for quantifying albumin. Using an independent prediction set, the R2 and root mean squared error of prediction between predicted and reference values of human serum albumin concentrations were 0.982 and 2.82, respectively. Here, we show that direct SERS spectroscopy has the sensitivity required for detecting clinically relevant concentrations of urinary albumin, a strategy that could be used in the future for the point-of-care screening of microalbuminuria.

Lipophilic marine biotoxins SERS sensing in solutions and in mussel tissue.

To detect and recognise three structurally related marine biotoxins responsible for the diarrheic shellfish poisoning (DSP) symptom, namely okadaic acid (OA), dinophysistoxin-1 (DTX-1) and dinophysistoxin-2 (DTX-2) respectively, as well as the structurally different yessotoxin (YTX), we developed a novel surface-enhanced micro-Raman scattering (micro-SERS) approach to investigate for the first time their micro-SERS signalling in solution and jointly analysed them in conjunction with the normal and toxic mussel tissue. YTX provided the main SERS feature surprisingly similar to DTX-1 and DTX-2, suggesting similar molecular adsorption mechanism with respect to the AgNPs. A fingerprint SERS band at 1017 cm-1 characteristic for the C-CH3 stretching in DTX-1 and DTX-2 and absent in OA SERS signal, allowed direct SERS discrimination of DTX-1,2 from OA. In acid form or as dissolved potassium salt, OA showed reproducible SERS feature for 0.81 µM to 84.6 nM concentrations respectively, while its ammonium salt slightly changed the overall SERS signature. The inherently strong fluorescence of the shellfish tissue, which hampers Raman spectroscopy analysis, further increases when toxins are present in tissue. Through SERS, tissue fluorescence is partially quenched. Artificially intoxicated mussel tissue with DSP toxins and incubated with AgNPs allowed direct SERS evidence of the toxin presence, opening a novel avenue for the in situ shellfish tracking and warning via micro-SERS. Natural toxic tissue containing 57.91 µg kg-1 YTX (LC-MS confirmed) was micro-SERS assessed to validate the new algorithm for toxins detection. We showed that a portable Raman system was able to reproduce the lab-based SERS results, being suitable for in situ raw seafood screening. The new approach provides an attractive, faster, effective and low-cost alternative for seafood screening, with economic, touristic and sustainable impact in aquaculture, fisheries, seafood industry and consumer trust.

Characterization of Clinically Relevant Fungi via SERS Fingerprinting Assisted by Novel Chemometric Models.

Nonculture-based tests are gaining popularity and upsurge in the diagnosis of invasive fungal infections (IFI) fostered by their main asset, the reduced analysis time, which enables a more rapid diagnosis. In this project, three different clinical isolates of relevant filamentous fungal species were discriminated by using a rapid (less than 5 min) and sensitive surface-enhanced Raman scattering (SERS)-based detection method, assisted by chemometrics. The holistic evaluation of the SERS spectra was performed by employing appropriate chemometric tools-classical and fuzzy principal component analysis (FPCA) in combination with linear discriminant analysis (LDA) applied to the first relevant principal components. The efficiency of the proposed robust algorithm is illustrated on the data set including three fungal isolates (Aspergillus fumigatus sensu stricto, cryptic A. fumigatus complex species, and Rhizomucor pusillus) that were isolated from patient materials. The accurate and reliable discrimination between species of common fungal pathogen strains suggest that the developed method has the potential as an alternative, spectroscopic-based routine analysis tool in IFI diagnosis.

Citrus fruits freshness assessment using Raman spectroscopy.

The freshness of citrus fruits commonly available in the market was non-destructively assessed by Raman spectroscopy. Intact clementine, mandarin and tangerine species were characterised concerning their carotenoids skin Raman signalling in a time course from the moment they were acquired as fresh stock, supplying the market, to the physical degradation, when they were no longer attractive to consumers. The freshness was found to strongly correlate to the peel Raman signal collected from the same area of the intact fruits in a time course of a maximum of 20days. We have shown that the intensity of the carotenoid Raman signal is indeed a good indicator of fruit freshness and introduced a Raman coefficient of freshness (CFresh), whose time course is linearly decreasing, with different slope for different citrus groups. Additionally, we demonstrated that the freshness assessment could be achieved using a portable Raman instrument. The results could have a strong impact for consumer satisfaction and the food industry.

Conformational Preference and Spectroscopical Characteristics of the Active Pharmaceutical Ingredient Levetiracetam.

The analysis of the possible conformers and the conformational change between solid and liquid states of a particular drug molecule are mandatory not only for describing reliably its spectroscopical properties but also for understanding the interaction with the receptor and its mechanism of action. Therefore, here we investigated the free-energy conformational landscape of levetiracetam (LEV) in gas phase as well as in water and ethanol, aiming to describe the 3-dimensional structure and energetic stability of its conformers. Twenty-two unique conformers were identified, and their energetic stability was determined at density functional theory B3LYP/6-31+G(2d,2p) level of theory. The 6 most stable monomers in water, within a relative free-energy window of 0.71 kcal mol-1 and clearly separated in energy from the remaining subset of 16 conformers, as well as the 3 most stable dimers were then used to compute the Boltzmann populations-averaged UV-Vis and NMR spectra of LEV. The conformational landscape in solution is distinctly different from that corresponding to gas phase, particularly due to the relative orientations of the butanamide group. Aiming to clarify the stability of the possible dimers of LEV, we also investigated computationally the structure of a set of 11 nonhydrated and hydrated homochiral hydrogen-bonded LEV dimers.

Conformational landscape and low lying excited states of imatinib.

The conformational changes of imatinib (IMT) are crucial for understanding the ligand-receptor interaction and its mechanism of action [Agofonov et al. (2014) Nature Struct Mol Biol 21:848-853]. Therefore, here we investigated the free energy conformational landscape of the free IMT base, aiming to describe the three-dimensional structures and energetic stability of its conformers. Forty-five unique conformers, within an energy window of 4.8 kcal mol(-1) were identified by a conformational search in gas-phase, at the B3LYP/6-31G(d) theoretical level. Among these, the 20 most stable, as well as 4 conformers resulting from optimization of experimental structures found in the two known polymorphs of IMT and in the c-Abl complex were further refined using the 6-31+G(d,p) basis set and the polarizable continuum solvation model. The most stable conformers in gas-phase and water exhibit a V-shaped structure. The major difference between the most stable free conformers and the bioactive conformers consists in the relative orientation of the pyrimidine-pyridine groups responsible for hydrogen bonding interactions in the ATP-binding pocket. The ratio of mole fractions corresponding to the two known (α and ß) polymorphic forms of IMT was estimated from the calculated thermochemical data, in quantitative agreement with the existing experimental data related to their solubility. The electronic absorption spectrum of this compound was investigated in water and explained based on the theoretical TD-DFT results, considering the Boltzmann population-averaged computed data at CAM-B3LYP/6-31+G(d,p) level of theory for the nine most stable conformers.

Surface mediated chiral interactions between cyclodextrins and propranolol enantiomers: a SERS and DFT study.

The nanoparticles mediated enantioselective recognition of propranolol enantiomers through native cyclodextrin complexation has been investigated by using surface-enhanced Raman spectroscopy (SERS). The highly efficient chiral recognition mechanism is based on a synergistic interaction between spherical noble metal nanoparticles, propranolol enantiomers and native cyclodextrins (CDs). Amongst the native cyclodextrins, ß-CD has the highest chiral recognition ability for propranolol enantiomers, due to its specific shape and cavity size, thus producing the largest difference between the recorded SERS spectra of the two hosted enantiomers. The molecular interaction mechanism responsible for enantioselectivity was furthermore proven by quantum chemical calculations based on density functional theory (DFT). The theoretical calculations and experimental SER spectra allowed the assignment of functional moieties involved in the chiral recognition mechanism. The most important factors governing the highly efficient chiral probing by SERS are the fundamentally different mechanism of interaction between the R- and S-enantiomers and ß-CD and the strength of interaction between the nanoparticle surface and the two propranolol-CD complexes. The role of metallic nanoparticles in the enantioselective recognition process has been experimentally evaluated by using silver and gold nanoparticles as SERS substrates, given their ability to interact differently with the complexes. The viability of this new method for chiral discrimination has been demonstrated for both substrates and could open new avenues for these kinds of applications.

Towards a receptor-free immobilization and SERS detection of urinary tract infections causative pathogens.

Based on molecular-specific surface-enhanced Raman scattering (SERS) spectroscopy we were able to discriminate between rough and smooth strains of Escherichia coli and Proteus mirabilis bacteria. For this purpose, bacteria have been immobilized through electrostatic forces by inducing a positive charge on the glass slide. This way, SERS spectra on bacterial biomass and also on single bacteria could be recorded in less than 2 h, by using concentrated silver nanoparticles as SERS-active substrate. Single-bacterium SERS spectral fingerprints showed to be sensitive to the presence of the O-antigen at strain level and to the microorganisms growth phase. By using principal component analysis (PCA) on the SERS spectra recorded from E. coli and P. mirabilis, these two uropathogens could be fairly discriminated.

Detection of thiabendazole applied on citrus fruits and bananas using surface enhanced Raman scattering.

Thiabendazole (TBZ) is a chemical fungicide and parasiticide largely used in food industry against mold and blight in vegetables and fruits during transportation and long term deposit. We investigated the possibility to detect and monitor the TBZ from the chemically treated bananas and citrus fruits available on Romanian market, using surface enhanced Raman spectroscopy (SERS) with a compact, portable, mini-Raman spectrometer. To assess the potential of the technique for fast, cheap and sensitive detection, we report the first complete vibrational characterization of the TBZ in a large pH and concentration range in conjunction with the density functional theory (DFT) calculations. From the relative intensity of the specific SERS bands as a function of concentration, we estimated a total amount of TZB as 78 mg/kg in citrus fruits, 13 times higher than the maximum allowed by current regulations, whereas in banana fruit the value was in the allowed limit.

Weakly bound PTCDI and PTCDA dimers studied by using MP2 and DFT methods with dispersion correction.

Potential energy curves along the inter-planar coordinates have been calculated for the dimers of two perylene derivatives (PTCDI and PTCDA) by using MP2 and dispersion corrected DFT (DFT-D) methods with B3LYP, B97 and PBE0 density functionals. The performance of dispersion-correcting potentials (DCPs) for describing intermolecular van der Waals interactions was also tested in conjunction with PBE0 and B971 functionals. Analytical potential energy curves were derived at different levels of theory by fitting the calculated data to modified Morse, Murrell-Sorbie, Buckingham and Lennard-Jones potentials. Potential energy surfaces for the two types of dimers were explored at the PBE0-DCP/6-31+G(d,p) level of theory in order to assess the effects of geometrical perturbations (displacements and/or rotations) on the stability of the dimers. Two minima were located for each perylene derivative, depending on the starting geometries of the dimers. Inter-monomer geometrical parameters of fully and partially optimized dimeric structures, as well as their relative stability, are discussed in comparison to available experimental data and other theoretical results on these or similar compounds.

Vibrational spectroscopic and DFT study of trimethoprim.

Structural investigations by different vibrational spectroscopic methods: FTIR, FT-Raman and surface-enhanced Raman scattering (SERS) spectroscopy, as well as density functional theory (DFT) calculations were performed on trimethoprim (5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine). A reliable assignment of vibrational IR, Raman and SERS bands was possible by a proper choice of model used in quantum chemical calculations. Based on SERS spectrum analysis it is shown that the molecule is adsorbed on the silver surface through the pyrimidine ring, in a perpendicular orientation. Two theoretical models were used in order to simulate the silver surface and the interaction with trimethoprim molecule, the accuracy of the models being evaluated by comparing the predicted bands position of the two complexes with the SERS result.