Mechanism of Pyridine Protonation in Water Clusters of Increasing Size

Parallelized Raman Difference Spectroscopy for the Investigation of Chemical Interactions

Raman spectroscopy provides an extremely high chemical selectivity. Raman difference spectroscopy is a technique to reveal even the smallest differences that occur due to weak interactions between substances and changes in the molecular structure. To enable parallelized and highly sensitive Raman difference spectroscopy in a microtiter-array, a diffractive optical element, a lens array, and a fiber bundle were integrated into a Raman spectroscopy setup in a unique fashion. The setup was evaluated with a microtiter-array containing pyridine-water complexes, and subwavenumber changes below the spectrometer's resolution could be resolved. The spectral changes were emphasized with two-dimensional correlation analysis. Density functional theory calculation and "atoms in molecule" analysis were performed to simulate the intermolecular long-range interactions between water and pyridine molecules and to get insight into the involved noncovalent interactions, respectively. It was found that by the addition of pyridine, the energy portion of hydrogen bonds to the total complexation energy between pyridine and water reduces. These results demonstrate the unique abilities of the new setup to investigate subtle changes due to biochemically important molecular interactions and opens new avenues to perform drug binding assays and to monitor highly parallelized chemical reactions.

Energy Dispersion in Pyridinium-Water Nanodroplets upon Irradiation

Postirradiation dissociation of molecular clusters has been mainly studied assuming energy redistribution in the entire cluster prior to the dissociation. Here, the evaporation of water molecules from out-of-equilibrium pyridinium-water cluster ions was investigated using the recently developed correlated ion and neutral time-of-flight (COINTOF) mass spectrometry technique in combination with a velocity-map imaging (VMI) device. This special setup enables the measurement of velocity distributions of the evaporated molecules upon high-velocity collisions with an argon atom. The distributions measured for pyridinium-water cluster ions are found to have two distinct components. Besides a low-velocity contribution, which corresponds to the statistical evaporation of water molecules after nearly complete redistribution of the excitation energy within the clusters, a high-velocity contribution is also found in which the molecules are evaporated before the energy redistribution is complete. These two different evaporation modes were previously observed and described for protonated water cluster ions. However, unlike in the case of pure water clusters, the low-velocity part of the distributions for pyridinium-doped water clusters is itself composed of two distinct Maxwell-Boltzmann distributions, indicating that evaporated molecules originate in this case from out-of-equilibrium processes. Statistical molecular dynamics simulations were performed to (i) understand the effects caused in the ensuing evaporation process by the various excitation modes at different initial cluster constituents and to (ii) simulate the distributions resulting from sequential evaporations. The presence of a hydrophobic impurity in water clusters is shown to impact water molecule evaporation due to the energy storage in the internal degrees of freedom of the impurity.

Ultrasensitive Picomolar Detection of Aqueous Acids in Microscale Fluorescent Droplets

We report on a fluorescent-droplet-based acid-sensing scheme that allows limits of detection below 100 pM for weak acids. The concept is based on a strong partitioning of acid from an aqueous phase into octanol droplets. Using salicylic acid as a demonstration, we show that at a high concentration, the acid partitions into the organic phase by a factor of 260, which is approximately consistent with literature values. However, at lower concentrations, we obtain a partition coefficient as high as 10⁶, which is partly responsible for the excellent sensing performance. The enhanced equilibrium partitioning is likely due to the interaction of the dissociated acid phase with the sensor dye employed for this work. The effect of droplet size was determined, after which we derived a simple model to predict the time dependence of the color change as a function of droplet size. This work shows that color-change fluorescent-droplet-based detection is a promising avenue that can lead to exceptional sensing performance from an aqueous analyte.

Pyrrole and Pyridine in the Water Environment-Effect of Discrete and Continuum Solvation Models

Properties of pyrrole and pyridine molecules upon different hydrations were investigated through density functional theory. Complexes of studied molecules with a cluster of 50 water molecules were considered, and the polarizable continuum model of solvation (PCM) was also taken into account. For comparative purposes, all mentioned calculations were repeated for single pyrrole and pyridine molecules and their complexes with one water molecule. Aromaticities of solvated pyrrole and pyridine rings were studied using several geometric- and electronic-based aromaticity criteria. Special attention was paid to studying the properties of formed hydrogen bonds between pyrrole or pyridine and either a single water molecule or several water molecules of the cluster. Overall, a comprehensive description of two very important heterocyclic compounds, that is, pyrrole and pyridine, in both discrete and continuum water solutions, is extensively presented.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

Fragment and cluster ions from gaseous and condensed pyridine produced under electron impact

The ion-distribution from condensed pyridine due to 2 keV electron impact shows hydrogenated fragments and clusters with m/z ≤ 320 u and shifts towards higher masses compared to the gas-phase fragmentation. The formation of a bond between the pyridine and a carbenium ion is crucial for the stability of the selected cluster ions.

Comparison of tetrel bonds in neutral and protonated complexes of pyridineTF3and furanTF3(T = C, Si, and Ge) with NH3

Protonation not only changes the primary interaction mode between α/β-furanCF₃/p-PyCF₃and NH₃but also prominently enhances the strength of the Si/Ge⋯N tetrel bond.

Temperature-responsive properties of poly(4-vinylpyridine) coatings: influence of temperature on the wettability, morphology, and protein adsorption

Poly(4-vinylpyridine)-grafted brushes demonstrate a thermal response of their wettability (stronger than that for spin-coated films), surface morphology, and protein adsorption.

DFT STUDY OF THE PROTONATION AND DEPROTONATION ENTHALPIES OF BENZOXAZOLE, 1,2-BENZISOXAZOLE AND 2,1-BENZISOXAZOLE AND IMPLICATIONS FOR THE STRUCTURES AND ENERGIES OF THEIR ADDUCTS WITH EXPLICIT WATER MOLECULES

Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.

Pulsating tubules from noncovalent macrocycles

Despite recent advances in synthetic nanometer-scale tubular assembly, conferral of dynamic response characteristics to the tubules remains a challenge. Here, we report on supramolecular nanotubules that undergo a reversible contraction-expansion motion accompanied by an inversion of helical chirality. Bent-shaped aromatic amphiphiles self-assemble into hexameric macrocycles in aqueous solution, forming chiral tubules by spontaneous one-dimensional stacking with a mutual rotation in the same direction. The adjacent aromatic segments within the hexameric macrocycles reversibly slide along one another in response to external triggers, resulting in pulsating motions of the tubules accompanied by a chiral inversion. The aromatic interior of the self-assembled tubules encapsulates hydrophobic guests such as carbon-60 (C(60)). Using a thermal trigger, we could regulate the C(60)-C(60) interactions through the pulsating motion of the tubules.

A new experimental setup designed for the investigation of irradiation of nanosystems in the gas phase: a high intensity mass-and-energy selected cluster beam

DIAM (Dispositif d'Irradiation d'Agrégats Moléculaires) is a new experimental setup devoted to investigate processes induced by irradiation at the nanoscale. The DIAM apparatus is based on a combination of techniques including a particle beam from high-energy physics, a cluster source from molecular and cluster physics, and mass spectrometry form analytical sciences. In this paper, we will describe the first part of the DIAM apparatus that consists of an ExB double spectrometer connected to a cluster ion source based on a continuous supersonic expansion in the presence of ionizing electrons. This setup produces high intensities of energy-and-mass selected molecular cluster ion beams (1000 s of counts s(-1)). The performance of the instrument will be shown through measurements of 6-8 keV beams of protonated water clusters, (H(2)O)(n)H(+) (n = 0-21) and mixed protonated (or deprotonated) water-pyridine cluster ions: PyrH(+)(H(2)O)(n) (n = 0-15), Pyr(2)H(+) (H(2)O)(n) (n = 0-9), and (Pyr-H)(+) (H(2)O).

Determination of Critical Indices by “Slow” Spectroscopy: NMR Shifts by Statistical Thermodynamics and Density Functional Theory Calculations

The temperature dependencies of NMR shifts in the critical region of two coexisting phases have been simulated using statistical thermodynamics and graph-theory consideration of equilibrium processes of molecular association. Microparameters of magnetic screening of various water and water/pyridine structures used in the statistical averaging have been evaluated by density functional theory calculations (PBE1PBE and B3PW91 functionals in the 6-311++G** basis set). The gauge-including atomic orbital (GIAO) approach has been applied to ensure gauge invariance of the results. Solvent effects were taken into account by a polarized continuum model (PCM). NMR shifts "order parameters" (Deltadelta = |delta+ - delta-|) and "diameters" (phidelta = |(delta+ + delta-)/2 - deltaC|, where delta+, delta-, and deltaC are the chemical shifts of coexisting phases and at the critical point respectively) have been calculated in each case close to the lower critical solution point (TL) and processed using linear regression analysis of Deltadelta approximately |T - TL| and phidelta approximately |T - TL| in the log-log plot. It has been shown that the critical index beta can be evaluated with high precision from the slope of Deltadelta = f(T - TL) at any realistic set of model input parameters. The slope of diameter has been found to depend on both input beta and alpha values. The obtained phidelta slopes (0.58-0.63) are very close to 2beta values. The results are discussed within the concept of complete scaling. Results of simulation are compared and supported by experimental NMR data for water/2,6-lutidine, acetic anhydride/n-heptane, and acetic anhydride/cyclohexane systems.

Effects of Hydrogen Bonding on the Ring Stretching Modes of Pyridine

The effects of hydrogen bonding on the ring stretching modes (both ring breathing and triangle) of pyridine are experimentally investigated using noisy light based coherent Raman scattering spectroscopy. Three systems, pyridine/formamide, pyridine/water, and pyridine/acetic acid, provide varying degrees of strength for the diluent-pyridine hydrogen bond complex. Formamide forms a relatively weaker hydrogen bond, while acetic acid essentially fully transfers a proton to pyridine. Both dilution studies and temperature studies are performed on the three systems. Together, these provide a broad context in which a very simple model for the electronic behavior of pyridine is formulated. This model is based on a molecular orbital picture and electrostatic arguments, and it well explains the observed experimental results. Additionally, a new mechanism for the line broadening of the ring breathing mode for the pyridine-water hydrogen bonded complex is proposed.