Effects of Hydrogen Bonding on the Ring Stretching Modes of Pyridine

Disentangling Acid-Base Chemistry through Blue Shifting Hydrogen Bond Contributions

The blue shifting of vibrational frequencies in hydrogen bonded molecules, as observed in aqueous environments, has been attributed to local partial charge transfer from solvation. Here, we extrapolate the blue shift model to the stronger ionic interactions between hydrogen bond acceptors associated with protonation through augmented pH levels and competitive interactions with counter ion pairing. The chemical model we utilize in this work is the aqueous pyridine-pyridinium equilibrium to characterize the blue shifts observed in the pyridinium chloride ionic system. The observed agreement between observed experimental and calculated spectral shifts shows that the blue shifting model can be extrapolated to stronger interactions and accurately describe the nature of the hydrogen bond.

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.

Noncovalent Bonding Caught in Action: From Amorphous to Cocrystalline Molecular Thin Films

We demonstrate the solvent-free amorphous-to-cocrystalline transformations of nanoscale molecular films. Exposing amorphous films to vapors of a haloarene results in the formation of a cocrystalline coating. This transformation proceeds by gradual strengthening of halogen-bonding interactions as a result of the crystallization process. The gas-solid diffusion mechanism involves formation of an amorphous metastable phase prior to crystallization of the films. In situ optical microscopy shows mass transport during this process, which is confirmed by cross-section analysis of the final structures using focused ion beam milling combined with scanning electron microscopy. Nanomechanical measurements show that the rigidity of the amorphous films influences the crystallization process. This surface transformation results in molecular arrangements that are not readily obtained through other means. Cocrystals grown in solution crystallize in a monoclinic centrosymmetric space group, whereas the on-surface halogen-bonded assembly crystallizes into a noncentrosymmetric material with a bulk second-order nonlinear optical response.

Structures of Pyridine-Water Clusters Studied with Infrared-Vacuum Ultraviolet Spectroscopy

The infrared (IR) spectra of the O-H stretching vibrations of pyridine-water clusters (Pyd)_m(H₂O)_n, with m, n = 1-4, have been investigated with infrared-vacuum ultraviolet (VUV) spectroscopy under a jet-cooled condition. The time-of-flight mass spectrum of (Pyd)_m(H₂O)_n⁺ by VUV ionization at ∼9 eV showed an unusual intensity pattern with very weak ion signals for m = 1 and 2 and stronger signals for m ≥ 3. This unusual mass pattern was explained by a drastic structural change of (Pyd)_m(H₂O)_n upon the VUV ionization, which was followed by the elimination of water molecules. Among the recorded IR spectra, only one spectrum monitored, (Pyd)₂⁺ cation, showed a well-resolved structure. The spectrum was analyzed by comparing with the simulated ones of possible stable isomers of (Pyd)₂(H₂O)_n, which were obtained with quantum-chemical calculations. Most of the calculated (Pyd)₂(H₂O)_n clusters had the characteristic structure in which H₂O or (H₂O)₂ forms a hydrogen-bonded bridge between two pyridines to form the π-stacked (Pyd)₂, and an additional H₂O molecule(s) extends the H-bonded network. The π-stacked (Pyd)₂(H₂O)_n moiety is very stable and is thought to exist as a local structure in a pyridine/water mixed solution. The Fermi resonance between the O-H stretch fundamentals and the overtones of the O-H bending vibrations in (Pyd)_m(H₂O)_n was found to be less pronounced in the case of (Pyd)_m(NH₃)_n studied previously.

Enhanced photoinduced mass migration in supramolecular azopolymers by H-bond driven positional constraint

Here we investigated the role of hydrogen bonding in the design of supramolecular azopolymers with a highly directional and constrained azobenzene-chain interaction involving the aromatic ring of the photoactive molecule, by exploiting the 2-aminopyrimidine/carboxylic acid supramolecular synthon as the tool for molecular recognition. We have shown that this approach is advantageous for producing affordable and versatile photopatternable azomaterials by complexation with polyacrylic acid (PAA). Molecular model complexes were successfully prepared and characterized by X-ray diffraction analysis and FTIR spectroscopy to reveal the multiple, non-ionic interaction occurring between the azobenzene units and the polymer chains. Surface photopatterning of thin films, driven by the typical mass migration phenomenon occurring in azopolymers, resulted strongly enhanced with increasing azobenzene content until equimolar composition. Results show that polymers with synthon-based azobenzenes markedly outperform single H-bonded systems bearing azomolecules with similar structure and electronic properties. We finally demonstrated that the azobenzene units can be easily extracted from a photopatterned film by a simple solvent rinse and without any chemical pre-treatment, leaving the periodicity of the inscribed surface relief gratings unaltered. This result was enabled by the orthogonal solubility of the components in the supramolecular system.

Quantitative characterisation of the ring normal modes. Pyridine as a study case

In the present work, the vibrational normal modes (NM) of pyridine were revisited. Quantum Chemical calculations were performed to help understand the true nature of some ring related vibrational normal modes (RNM) and how they may be correlated with the electronic structure on the ring. The 27 vibrational normal modes were decomposed into the molecular internal coordinates, and the interest was focused on 7 of them, involving the in-plane ring motion. The electronic structure was analysed through frontier Molecular Orbitals (MO), maps of Molecular Electrostatic Potential surfaces (MEPs) and Natural Bond Orbital (NBO) analysis in a dynamic manner, wherein, each vibration was scanned. The present investigation is aimed to provide the Reader with a quantitative characterisation of the RNMs of pyridine.

Coherent Anti-Stokes-Stokes Raman Cross-Correlation Spectroscopy: Asymmetric Frequency Shifts in Hydrogen-Bonded Pyridine-Water Complexes

Hydrogen bonding is a vital molecular interaction for bio-molecular systems, yet deep understanding of its ways of creating various complexes requires extensive empirical testing. A hybrid femtosecond/picosecond coherent Raman spectroscopic technique is applied to study pyridine-water complexes. Both the coherent Stokes and anti-Stokes Raman spectra are recorded simultaneously as the concentration of water in pyridine varied. A 3 ps and 10 cm^-1 narrowband probe pulse enables us to observe well-resolved Raman spectra. The hydrogen bonding between pyridine and water forms the complexes that have altered vibrational frequencies. These red and blue shifts were observed to be uneven. This asymmetry was result of the generated background nonlinear optical processes of pyridine-water complexes. This asymmetry tends to disappear as probe pulse further delayed attaining background-free coherent Raman spectra. For better visualization, spectral analyses both traditional two-dimensional correlation spectroscopy and recent second-order correlation functions defined in frequency domain are employed. Recognized as a label-free and background-free technique, the coherent Raman spectroscopy, complemented with a known high-resolution spectroscopic correlation analysis, has potential in studying the hydrogen-bonded pyridine-water complexes. These complexes are of great biological importance both due to the ubiquitous nature of hydrogen bonds and due to the close resemblance to chemical bases in macro-biomolecules.

Self-healing and tough GO-supported hydrogels preparedviasurface-initiated ATRP and photocatalytic modification

Hydrogels with the properties of self-healing, toughness, stiffness and strength have great potential for use in smart materials.

The impact on the ring related vibrational frequencies of pyridine of hydrogen bonds with haloforms – a topology perspective

An intermolecular ring structure is identified for the hydrogen bonding system of pyridine and haloforms.

The origin of the conductivity maximum vs. mixing ratio in pyridine/acetic acid and water/acetic acid

Explanations are provided for the first time for the historically known locations of electrical conductivity maxima versus mixing ratio (mole fraction of acid, x_A) in mixtures of (i) acetic acid with water and (ii) acetic acid with pyridine. To resolve the question for the second system, density-functional-based molecular dynamic simulations were performed, at 1:1, 1:2, 1:3, 1:5, and 1:15 mixing ratios, to gain vital information about speciation. In a zeroth-order picture, the degree of ionization (and hence conductivity) would be maximal at x_A = 0.5, but these two examples see this maximum shifted to the left (water/acetic acid, x_A^max = 0.06), due to improved ion stability when the effective dielectric constant is high (i.e., water-rich mixtures), or right (pyridine/acetic acid x_A^max = 0.83), due to improved acetate stability via "self-solvation" with acetic acid molecules (i.e., acid-rich mixtures) when the dielectric constant is low. A two-parameter equation, with theoretical justification, is shown to reproduce the entire 0 < x_A < 1 range of data for electrical conductivity for both systems. Future work will pursue the applicability of these equations to other amine/carboxylic acid mixtures; preliminary fits to a third system (trimethylamine/acetic acid) give curious parameter values.

Intermolecular Interactions of Pyridine in Liquid Phase and Aqueous Solution Studied by Soft X-ray Absorption Spectroscopy

Intermolecular interactions of pyridine in liquid and in aqueous solution are studied by using soft X-ray absorption spectroscopy (XAS) at the C, N, and O K-edges. XAS of liquid pyridine shows that the N 1s→π* peak is blue shifted and the C 1s→π* peak of the meta and para sites is red shifted, respectively, as compared with XAS of pyridine gas. These shifts in liquid are smaller than those in clusters, indicating that the intermolecular interaction of liquid pyridine is weaker than that of pyridine cluster, as supported by the combination of quantum chemical calculations of the core excitation and molecular dynamics simulations of the liquid structure. On the other hand, XAS spectra of aqueous pyridine solutions (C5H5N)x(H2O)1−x measured at different molar fractions show that in the pyridine rich region, x>0.7, the C and N 1s→π* peak energies are not so different from pure liquid pyridine (x=1.0). In this region, antiparallel displaced structures of pyridine molecules are dominant as in pure pyridine liquid. In the O K-edge XAS, the pre-edge peaks sensitive to the hydrogen bond (HB) network of water molecules show the red shift of −0.15 eV from that of bulk water, indicating that small water clusters with no large-scale HB network are formed in the gap space of structured pyridine molecules. In the water rich region, 0.7>x, the N 1s→π* peaks and the O 1s pre-edge peaks are blue shifted, and the C 1s→π* peaks of the meta and para sites are red-shifted by increasing molar fraction of water. The HB network of bulk water is dominant, but quantum chemical calculations indicate that small pyridine clusters with the HB interaction between the H atom in water and the N atom in pyridine are still existent even in very dilute pyridine solutions.

Discrimination between hydrogen bonding and protonation in the spectra of a surface-enhanced Raman sensor

Adsorbed mercaptopyridine can sense hydrogen-bonding because the ring breathing mode has a different frequency from bare and protonated species.

Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach

The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Two-dimensional electronic spectroscopy using incoherent light: theoretical analysis

Electronic energy transfer in photosynthesis occurs over a range of time scales and under a variety of intermolecular coupling conditions. Recent work has shown that electronic coupling between chromophores can lead to coherent oscillations in two-dimensional electronic spectroscopy measurements of pigment-protein complexes measured with femtosecond laser pulses. A persistent issue in the field is to reconcile the results of measurements performed using femtosecond laser pulses with physiological illumination conditions. Noisy-light spectroscopy can begin to address this question. In this work we present the theoretical analysis of incoherent two-dimensional electronic spectroscopy, I((4)) 2D ES. Simulations reveal diagonal peaks, cross peaks, and coherent oscillations similar to those observed in femtosecond two-dimensional electronic spectroscopy experiments. The results also expose fundamental differences between the femtosecond-pulse and noisy-light techniques; the differences lead to new challenges and new opportunities.

Effect of deuteration on hydrogen bonding: a comparative concentration dependent Raman and DFT study of pyridine in CH₃OH and CD₃OD and pyrimidine in H₂O and D₂O

The relative effect of hydrogen bonding of pyrimidine (Pyr) in H(2)O/D(2)O and pyridine (Py) in CH(3)OH/CD(3)OD has been analyzed using Raman Difference Spectroscopic (RDS) technique and DFT calculations. This study is focused on analyzing the concentration dependent variation of linewidth, peak position and intensity of ring breathing mode of Py and Pyr. The ring breathing mode of Pyr in H(2)O and D(2)O has three components; due to free Pyr, lighter complexes of mPyr+nH(2)O/D(2)O and heavier complexes of mPyr+nH(2)O/D(2)O. The pyridine molecules, however, show only two components in CH(3)OH and CD(3)OD. Of these two components, one corresponds to free Py and the other inhomogeneously broadened profile corresponds to all mPy+nCH(3)OH/CD(3)OD complexes. The variation of peak position and linewidth establishes the role of dipole moment of complexes and the diffusion in the mixture. In case of CD(3)OD solution splitting was observed in ∼1030 cm(-1) band of Py, where an additional band at ∼1034 cm(-1) appears at x(Py) ≤ 0.4. However, this band remains single at all concentrations in case of CH(3)OH solvent.

Time-resolved surface-enhanced coherent sensing of nanoscale molecular complexes

Nanoscale real-time molecular sensing requires large signal enhancement, small background, short detection time and high spectral resolution. We demonstrate a new vibrational spectroscopic technique which satisfies all of these conditions. This time-resolved surface-enhanced coherent anti-Stokes Raman scattering (tr-SECARS) spectroscopy is used to detect hydrogen-bonded molecular complexes of pyridine with water in the near field of gold nanoparticles with large signal enhancement and a fraction of a second collection time. Optimal spectral width and time delays of ultrashort laser pulses suppress the surface-enhanced non-resonant background. Time-resolved signals increase the spectral resolution which is limited by the width of the probe pulse and allow measuring nanoscale vibrational dephasing dynamics. This technique combined with quantum chemistry simulations may be used for the investigation of complex mixtures at the nanoscale and surface environment of artificial nanostructures and biological systems.

Hydrogen-Bonding between Pyrimidine and Water: A Vibrational Spectroscopic Analysis

We present an experimental and a theoretical study on hydrogen-bonding between pyrimidine and water as the H-donor. The degree of hydrogen-bonding in this binary system varies with mixture composition. This was monitored experimentally by polarization-resolved linear Raman spectroscopy with the pyrimidine ring breathing mode nu1 as a marker band. A subsequent quantitative line shape analysis of the isotropic Raman intensity for 24 pyrimidine/water mixtures clearly revealed a splitting into three spectral components upon dilution with water. The two additional peaks have been assigned to distinct groups of hydrogen-bonded species that differ in the number of pyrimidine nitrogen atoms (N) involved in hydrogen-bonding to water hydrogen atoms (H). From the integrated Raman intensities for "free" and "hydrogen-bonded" pyrimidine, a concentration profile for these species was established. Our assignments and interpretations are supported by quantum mechanical calculations of structures and by vibrational spectra for pyrimidine and 10 pyrimidine/water complexes with increasing water content. Also, accurate structure-spectra correlations for different cluster subgroups have been determined; within each particular cluster subgroup the water content varies, and a perfect negative correlation between NH hydrogen-bond distances and nu1 wavenumbers was observed.