Charge transfer and blue shifting of vibrational frequencies in a hydrogen bond acceptor

Elucidating adsorption mechanisms of benzalkonium chlorides (BACs) on polypropylene and polyethylene terephthalate microplastics (MPs): Effects of BACs alkyl chain length and MPs characteristics

Since the onset of the COVID-19 pandemic, there has been an increase in the use of disposable plastics and disinfectants. This study systematically investigated the adsorption behavior and mechanisms of benzalkonium chlorides (BACs), commonly used disinfectants, on polypropylene (PP) and polyethylene terephthalate (PET) microplastics (MPs), considering various factors, such as characteristics of MPs, alkyl chain length of BACs, and environmental conditions. Our results demonstrated a higher adsorption capacity for PP-MPs with relatively hydrophobic properties compared to PET-MPs, where longer alkyl chains in BACs (i.e., higher octanol-water partition coefficients, Kow) significantly enhanced adsorption through hydrophobic interactions. The inverse relationship between particle size of MPs and adsorption was evident. While changes in pH minimally affected adsorption on PP-MPs, adsorption on PET-MPs increased with rising pH, highlighting the influence of pH on electrostatic interactions. Moreover, MP aging with UV/H2O2 amplified BAC adsorption on PP-MPs due to surface oxidation and fragmentation, whereas the properties of PET-MPs remained unaltered, resulting in unchanged adsorption capacities. Spectroscopy studies and density functional theory (DFT) calculations confirmed hydrophobic and electrostatic interactions as the primary adsorption mechanisms. These findings improve our understanding of MPs and BACs behavior in the environment, providing insights for environmental risk assessments related to combined pollution.

Probing halogen bonding interactions between heptafluoro-2-iodopropane and three azabenzenes with Raman spectroscopy and density functional theory

The potential formation of halogen bonded complexes between a donor, heptafluoro-2-iodopropane (HFP), and the three acceptor heterocyclic azines (azabenzenes: pyridine, pyrimidine, and pyridazine) is investigated herein through normal mode analysis via Raman spectroscopy, density functional theory, and natural electron configuration analysis. Theoretical Raman spectra of the halogen bonded complexes are in good agreement with experimental data providing insight into the Raman spectra of these complexes. The exhibited shifts in vibrational frequency of as high as 8 cm^-1 for each complex demonstrate, in conjunction with NEC analysis, significant evidence of charge transfer from the halogen bond acceptor to donor. Here, an interesting charge flow mechanism is proposed involving the donated nitrogen lone pair electrons pushing the dissociated fluorine atoms back to their respective atoms. This mechanism provides further insight into the formation and fundamental nature of halogen bonding and its effects on neighboring atoms. The present findings provide novel and deeper characterization of halogen bonding with applications in supramolecular and organometallic chemistry.

Raman Spectroscopic and Quantum Chemical Investigation of the Pyridine-Borane Complex and the Effects of Dative Bonding on the Normal Modes of Pyridine

The pyridine-borane (PyBH₃) complex was analyzed by Raman vibrational spectroscopy and density functional theory to elucidate its structural and vibrational properties and to compare these with those for neat pyridine (Py). The borane-nitrogen (BN) bond length, the BN dative bond stretching frequency, and the effects of dative-bonded complex formation on Py are presented. Rather than having a single isolated stretching motion, the complex exhibits multiple BN dative bond stretches that are coupled to Py's vibrations. These modes exhibit large shifts that are higher in energy relative to neat Py, similar to previous observations of Py/water mixtures. However, significantly higher charge transfer was observed in the dative-bonded complex when compared to the hydrogen-bonded complex with water. A linear relationship between charge transfer and shifts to higher frequencies of pyridine's vibrational modes agrees well with earlier observations. The present work is of interest to those seeking a stronger relationship between charge-transfer events and concomitant changes in molecular properties.

Opposite Raman Shift of Ring Stretching Dependent on the Coordinated Silver Volume in Surface-Enhanced Raman Spectroscopy of Polypyrrole

Surface-enhanced Raman spectroscopy (SERS) can sense some molecules in a nondestructive manner. Using SERS, we investigate the shifts in the Raman peaks of polypyrrole (PPy) with two different coordinated silver (Ag) structures, Ag nanoparticles (NPs) and Ag dendrite film. The SERS spectrum of PPy with Ag NPs presents a ring-stretching peak that is red-shifted compared to the ring-stretching peak in the Raman spectrum of PPy. In contrast, the spectrum of the PPy with the Ag dendrite film exhibits a blue-shifted ring stretching peak. The various coordinated Ag nanostructures result in opposite Raman shifts of the ring stretching peak; this phenomenon has been investigated and confirmed by density functional theory (DFT) calculations of the Raman shift of the pyrrole (Py) molecule with a Ag layer (SERS of PPy with Ag NPs) and that of a charge-transferred Py molecule (SERS of PPy with Ag dendrite films). This result demonstrates that DFT calculations can be an effective tool to scrutinize Raman shifts in SERS.

Elucidation of pH impacts on monosubstituted benzene derivatives using normal Raman and surface-enhanced Raman scattering

Raman spectral vibrational frequencies are used to probe the local chemical environment surrounding molecules in solution and adsorbed to gold nanostars. Herein, the impacts of functional group protonation on monosubstituted benzene derivatives with amine, carboxylic acid, or hydroxide are evaluated. Changes in binding affinity and orientation are apparent by evaluating systematic variations in vibrational frequencies. Notably, the electron donating abilities of these functional groups influence the vibrational frequency of the ring breathing mode, thus leading to improved spectral interpretation. Furthermore, gold nanostars are used to investigate the impact of molecular protonation on the adsorption of benzoic acid/benzoate to gold. The changes in molecular protonation are measured using zeta potential and the surface-sensitive technique, surface-enhanced Raman scattering. These methods reveal that pH variations induce carboxylate protonation and electron redistribution that weaken molecular affinity, thereby causing the molecule to adopt a perpendicular to parallel orientation with respect to the nanostar surface. Functional group identity influences the ring breathing mode frequency as a function of changes in electron donation from the functional group to the ring in solution as well as molecular affinity to and orientation on gold. This exploitation of vibrational frequencies facilitates the elucidation of molecule behavior in complex systems.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

A Raman Spectroscopic and Computational Study of New Aromatic Pyrimidine-Based Halogen Bond Acceptors

Two new aromatic pyrimidine-based derivatives designed specifically for halogen bond directed self-assembly are investigated through a combination of high-resolution Raman spectroscopy, X-ray crystallography, and computational quantum chemistry. The vibrational frequencies of these new molecular building blocks, pyrimidine capped with furan (PrmF) and thiophene (PrmT), are compared to those previously assigned for pyrimidine (Prm). The modifications affect only a select few of the normal modes of Prm, most noticeably its signature ring breathing mode, ν1. Structural analyses afforded by X-ray crystallography, and computed interaction energies from density functional theory computations indicate that, although weak hydrogen bonding (C–H···O or C–H···N interactions) is present in these pyrimidine-based solid-state co-crystals, halogen bonding and π-stacking interactions play more dominant roles in driving their molecular-assembly.

The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C2H2⋯HF and C2H4⋯HF small dimers

The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C₂H₂⋯(HF), C₂H₂⋯2(HF), C₂H₂⋯4(HF), C₂H₄⋯(HF), C₂H₄⋯2(HF) and C₂H₄⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).

Conformational Changes and Charge Transfer in Biomolecules Resolved Using Dynamic Enhanced Raman Correlation Spectroscopy

In this contribution, we report that conformational changes of molecules that are often buried in a wide-distributed Gaussian distribution can be discerned by analyzing the dynamics of specific Raman lines. We investigate the pertinence of the auto- and cross-correlation functions applied to the dynamics of three Raman lines of an amino acid, the tryptophan. The cross-correlation between intensity and the Raman band is an indicator of the charge transfer during the diffusion limited reaction of tryptophan and the gold surface. The Péclet number Pe can provide a valuable indicator of the convective and/or diffusive features of each Raman band. Adsorption induced conformation changes can be identified using the autocorrelation of the multiples states within the Raman band centered at 1550 cm^-1.

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.

Noncovalent Interactions between Trimethylamine N-Oxide (TMAO), Urea, and Water

Trimethylamine N-oxide (TMAO) and urea are two important osmolytes with their main significance to the biophysical field being in how they uniquely interact with proteins. Urea is a strong protein destabilizing agent, whereas TMAO is known to counteract urea's deleterious effects. The exact mechanisms by which TMAO stabilizes and urea destabilizes folded proteins continue to be debated in the literature. Although recent evidence has suggested that urea binds directly to amino acid side chains to make protein folding less thermodynamically favored, it has also been suggested that urea acts indirectly to denature proteins by destabilizing the surrounding hydrogen bonding water networks. Here, we elucidate the molecular level mechanism of TMAO's unique ability to counteract urea's destabilizing nature by comparing Raman spectroscopic frequency shifts to the results of electronic structure calculations of microsolvated molecular clusters. Experimental and computational data suggest that the addition of TMAO into an aqueous solution of urea induces blue shifts in urea's H-N-H symmetric bending modes, which is evidence for direct interactions between the two cosolvents.

Blue- and Red-Shifting Hydrogen Bonding: A Gas Phase FTIR and Ab Initio Study of RR'CO···DCCl3 and RR'S···DCCl3 Complexes

Blue-shifting H-bonded (C-D···O) complexes between CDCl₃ and CH₃HCO, (CH₃)₂CO, and C₂H₅(CH₃)CO, and red-shifting H-bonded (C-D···S) complexes between CDCl₃ with (CH₃)₂S and (C₂H₅)₂S have been identified by Fourier transform infrared spectroscopy in the gas phase at room temperature. With increasing partial pressure of the components, a new band appears in the C-D stretching region of the vibrational spectra. The intensity of this band decreases with an increase in temperature at constant pressure, which provides the basis for identification of the H-bonded bands in the spectrum. The C-D stretching frequency of CDCl₃ is blue-shifted by +7.1, +4, and +3.2 cm^-1 upon complexation with CH₃HCO, (CH₃)₂CO, and C₂H₅(CH₃)CO, respectively, and red-shifted by -14 and -19.2 cm^-1 upon complexation with (CH₃)₂S and (C₂H₅)₂S, respectively. By using quantum chemical calculations at the MP2/6-311++G** level, we predict the geometry, electronic structural parameters, binding energy, and spectral shift of H-bonded complexes between CDCl₃ and two series of compounds named RCOR' (H₂CO, CH₃HCO, (CH₃)₂CO, and C₂H₅(CH₃)CO) and RSR' (H₂S, CH₃HS, (CH₃)₂S, and (C₂H₅)₂S) series. The calculated and observed spectral shifts follow the same trends. With an increase in basicity of the H-bond acceptor, the C-D bond length increases, force constant decreases, and the frequency shifts to the red from the blue. The potential energy scans of the above complexes are done, which show that electrostatic attraction between electropositive D and electron-rich O/S causes bond elongation and red shift, and the electronic and nuclear repulsions lead to bond contraction and blue shifts. The dominance of the two opposing forces at the equilibrium geometry of the complex determines the nature of the shift, which changes both in magnitude and in direction with the basicity of the hydrogen-bond acceptor.

Interactions of Gaseous 2-Chlorophenol with Fe3+-Saturated Montmorillonite and Their Toxicity to Human Lung Cells

The interactions of gaseous 2-chlorophenol with Fe³⁺-saturated montmorillonite particles in a gas-solid system were investigated to simulate the reactions of mineral dusts with volatile organic pollutants in the atmosphere. Results suggested that Fe³⁺-saturated montmorillonite mediated the dimerization of gaseous 2-chlorophenol to form hydroxylated polychlorinated biphenyl, hydroxylated polychlorinated diphenyl ether, and hydroxylated polychlorinated dibenzofuran. The toxicity of Fe³⁺-montmorillonite particles to A549 human lung epithelial cells before and after interaction with 2-chlorophenol was examined to explore their adverse impact on human health. Based on cell morphological analysis, cytotoxicity tests, and Fourier-transform infrared imaging spectra, surface-catalyzed reactions of Fe³⁺-montmorillonite with 2-chlorophenol increased the toxicity of montmorillonite particle on A549 cells. This was supported by increased cellular membrane permeability, the release of extracellular lactate dehydrogenase, and cell damages on cellular DNA, proteins, and lipids. Since mineral dusts are important components of particulate matter, our results help to understand the interactions of volatile organic pollutants with particulate matter in the atmosphere and their adverse impacts on human health.

Quantifying the Effects of Halogen Bonding by Haloaromatic Donors on the Acceptor Pyrimidine

The effects of intermolecular interactions by a series of haloaromatic halogen bond donors on the normal modes and chemical shifts of the acceptor pyrimidine are investigated by Raman and NMR spectroscopies and electronic structure computations. Halogen-bond interactions with pyrimidine's nitrogen atoms shift normal modes to higher energy and upfield shift ¹ H and ¹³ C NMR peaks in adjacent nuclei. This perturbation of vibrational normal modes is reminiscent of the effects of hydrogen bonded networks of water, methanol, or silver on pyrimidine. The unexpected observation of vibrational red shifts and downfield ¹³ C NMR shifts in some complexes suggests that other intermolecular forces such as π interactions are competing with halogen bonding. Natural bond orbital analyses indicate a wide range of charge transfer is possible from pyrimidine to different haloaromatic donors and computed halogen bond binding energies can be larger than a typical hydrogen bond. These results emphasize the importance in strategic selection of substituents and electron withdrawing groups in developing supramolecular structures based on halogen bonding.

New insights about the hydrogen bonds formed between acetylene and hydrogen fluoride: π⋯H, C⋯H and F⋯H

A theoretical study of hydrogen bond strength and bond properties in the C₂H₂⋯(HF)-T, C₂H₂⋯2(HF)-T, C₂H₂⋯2(HF), C₂H₂⋯3(HF) and C₂H₂⋯4(HF) complexes was carried out at the B3LYP/6-311++G(d,p) theory level. In these systems, a strength competition between the π⋯H and C⋯H interactions was examined. Specifically the F⋯H hydrogen bond, its properties were studied through a comparison between the hydrogen fluoride and the higher-order complexes (trimer, tetramer and pentamer). Regarding the electronic properties, the hydrogen bond strength could not be determined by the supermolecule approach. Thus, the hydrogen bond energies were computed via NBO calculations. Additionally to NBO, the ChelpG charge calculations were used to interpret the intermolecular charge transfer. The QTAIM integrations were useful to predict the covalent character of the π⋯H, C⋯H and F⋯H hydrogen bonds. Moreover, values of hybrid orbitals (s and p) and atomic radii were also determined in order to justify the red shifts in the stretch frequencies of the HF bonds.

Vibrational solvatochromism. III. Rigorous treatment of the dispersion interaction contribution

A rigorous first principles theory of vibrational solvatochromism including the intermolecular dispersion interaction, which is based on the effective fragment potential method, is developed. The present theory is an extended version of our previous vibrational solvatochromism model that took into account the Coulomb, exchange-repulsion, and induction interactions. We show that the frequency shifts of the amide I mode of N-methylacetamide in H2O and CDCl3, when combined with molecular dynamics simulations, can be quantitatively reproduced by the theory, which indicates that the dispersion interaction contribution to the vibrational frequency shift is not always negligibly small. Nonetheless, the reason that the purely Coulombic interaction model for vibrational solvatochromism works well for describing amide I mode frequency shifts in polar solvents is because the electrostatic contribution is strong and highly sensitive to the relative orientation of surrounding solvent molecules, which is in stark contrast with polarization, dispersion, and exchange-repulsion contributions. It is believed that the theory presented and discussed here will be of great use in quantitatively describing vibrational solvatochromism and electrochromism of infrared probes in not just polar solvent environments but also in biopolymers such as proteins.

Competition between Hydrophilic and Argyrophilic Interactions in Surface Enhanced Raman Spectroscopy

The competition for binding and charge-transfer (CT) from the nitrogen containing heterocycle pyrimidine to either silver or to water in surface enhanced Raman spectroscopy (SERS) is discussed. The correlation between the shifting observed for vibrational normal modes and CT is analyzed both experimentally using Raman spectroscopy and theoretically using electronic structure theory. Discrete features in the Raman spectrum correspond to the binding of either water or silver to each of pyrimidine's nitrogen atoms with comparable frequency shifts. Natural bond orbital (NBO) calculations in each chemical environment reveal that the magnitude of charge transfer from pyrimidine to adjacent silver atoms is only about twice that for water alone. These results suggest that the choice of solvent plays a role in determining the vibrational frequencies of nitrogen containing molecules in SERS experiments.

The study of secondary effects in vibrational and hydrogen bonding properties of 2- and 3-ethynylpyridine and ethynylbenzene by IR spectroscopy

Weak hydrogen bonds formed by 2- and 3-ethynylpyridine and ethynylbenzene with trimethylphosphate and phenol were characterized by IR spectroscopy and DFT calculations (B3LYP/6-311++G(d, p)). The structure and stability of ethynylpyridines and ethynylbenzene in the gas phase and in the complexes with trimethylphosphate and phenol are discussed in terms of geometry and electronic charge redistribution. Anharmonic effects are taken into account when calculating vibrational wavenumbers of these systems what lead to partial improvement of agreement with experiment. The changes in the electronic charge distribution are behind the frequency shifts of the CC stretching in opposite direction depending on the role the ethyne molecule has in a hydrogen bonded complex (Δν̃=+9 cm(-1) in trimethylphosphate complexes, Δν̃=-3 cm(-1) in phenol complexes). The association constants were determined by keeping the concentrations of proton donors approximately constant and low enough to avoid self-association and the proton acceptors were present in excess. The values obtained for the association constants and enthalpy changes in C2Cl4 (for trimethylphosphate complexes K≈0.5-1.0 mol(-1)dm(3) and -ΔrH≈6-8 kJ mol(-1), for phenol complexes K≈20-40 mol(-1) dm3-ΔrH≈17-22 kJ mol(-1)) are in good agreement with literature data.

Photoelectron spectroscopic and computational study of hydrated pyrimidine anions

The stabilization of the pyrimidine anion by the addition of water molecules is studied experimentally using photoelectron spectroscopy of mass-selected hydrated pyrimidine clusters and computationally using quantum-mechanical electronic structure theory. Although the pyrimidine molecular anion is not observed experimentally, the addition of a single water molecule is sufficient to impart a positive electron affinity. The sequential hydration data have been used to extrapolate to -0.22 eV for the electron affinity of neutral pyrimidine, which agrees very well with previous observations. These results for pyrimidine are consistent with previous studies of the hydrated cluster anions of uridine, cytidine, thymine, adenine, uracil, and naphthalene. This commonality suggests a universal effect of sequential hydration on the electron affinity of similar molecules.

Electron transfer in pnicogen bonds

As a new type of noncovalent interactions, pnicogen bond between a VA group element (N, P, and As) and an electron donor (Lewis base) has grabbed attention in recent several years. Here we employ the block-localized wave function (BLW) based energy decomposition scheme to probe the bonding nature in a series of substituted phosphines X(n)PH(3-n) complexed with ammonia. As the BLW method can derive the optimal monomer orbitals in a complex with the electron transfer among monomers quenched, we can effectively examine the HOMO-LUMO interaction in these pnicogen bonding systems. Among various energy components, electron transfer energy together with the polarization energy dominates the pnicogen bonding energy. Although usually it is assumed that the electron transfer from ammonia to substituted phosphines occurs in the form of n → σ*(XP) hyperconjugative interaction, we identify a kind of new pathway when X = NO2 and CN, i.e., n → dπ*, which results from the interaction between the π orbital of cyano or nitro substituent and d orbitals on P. But still this picture of electron transfer using a single pair of orbitals is greatly simplified, as the electron density difference (EDD) maps corresponding to the overall electron transfer processes show the accumulation of electron density on the P side opposite to the X-P bond, with insignificant or even negligible gain of electron density on the substituent group side. Thus, the EDD maps tend to support the concept of σ-hole in pnicogen bonds.