Hydrogen bonding in the carboxylic acid–aldehyde complexes

Synthesis and characterization of nitrogen-doped-MWCNT@cobalt oxide for nerve agent simulant detection

Organophosphorus nerve agents are toxic compounds that disrupt neuromuscular transmission by inhibiting the neurotransmitter enzyme, acetylcholinesterase, leading to rapid death. A hybrid composite was synthesized using a hydrothermal process for the early detection of dimethyl methyl phosphonate (DMMP), a simulant of the G-series nerve agent, sarin. Quartz crystal microbalance (QCM) and surface acoustic wave (SAW) sensors were used as detectors. Nitrogen-doped multiwalled carbon nanotubes (N-MWCNTs), cobalt oxide (Co3O4), and N-MWCNT@Co3O4 were compared to detect DMMP concentrations of 25-150 ppm. At 25 ppm, the differential frequencies (Δf) of the N-MWCNT, Co3O4, and N-MWCNT@Co3O4 sensors were 5.8, 2.3, and 99.5 Hz, respectively. The selectivity results revealed a preference for the DMMP rather than potential interference. The coefficients of determination (R2) of the N-MWCNT, Co3O4, and N-MWCNT@Co3O4 sensors for detecting 25-150 ppm DMMP were 0.983, 0.986, and 0.999, respectively. The response times of the N-MWCNT, Co3O4, and N-MWCNT@Co3O4 sensors for detecting 100 ppm DMMP were 25, 27, and 34 s, respectively, while the corresponding recovery times were 85, 105, and 181 s. The repeatability results revealed the reversible adsorption and desorption phenomena for the fixed DMMP concentration of 100 ppm. These unique findings show that synthesized materials can be used to detect organophosphorus nerve agents.

Role of O–H⋯O/S conventional hydrogen bonds in considerable Csp2–H blue-shift in the binary systems of acetaldehyde and thioacetaldehyde with substituted carboxylic and thiocarboxylic acids

The presence of O–H⋯O/S conventional hydrogen bonds in the complex governs a significant blue shift of Csp2–H bonds.

Gas-phase hydration of nopinone: the interplay between theoretical methods and experiments unveils the conformational landscape

The structure of microsolvated nopinone formed in the supersonic jet expansion is investigated in the gas phase. The rotational spectra of nopinone(H₂O)_n (n = 1, 2, 3) were analysed by means of Fourier transform microwave spectroscopy. In the present study, three monohydrates, two dihydrates and two trihydrates were observed and characterized. The observed structures are the lowest energy conformers predicted by quantum chemical calculations. In all the observed hydrates of nopinone, water was found to be linked to the ketone group (C[double bond, length as m-dash]O) with a strong hydrogen bond (O_NOPH_W) and finishing with a dispersive one (O_WH_NOP). The structure of nopinone was found to alter the structure of water dimer and water trimer, which make nopinone be surrounded with a chain of water molecules. A remarkable decrease in the H-bonding length was observed when the number of attached water molecules is increased. Different DFT and ab initio calculations at the equilibrium structure allowed the identification of the observed conformers. Evaluation of the B3LYP-D3 and ωB97X-D results revealed deficiencies in reproducing the structure of one observed monohydrated structure while MP2 and M06-2X reproduce all the three observed structures. A comparison with similar bicyclic ketones highlights how a small change in the bicyclic ring leads to different effects in the microsolvation of biogenic VOCs. This study presents the first step of molecular aggregation to understand the atmospheric formation of aerosols at the molecular scale.

A theoretical study of hydrogen-bonded molecular clusters of sulfuric acid and organic acids with amides

Amides, a series of significant atmospheric nitrogen-containing volatile organic compounds (VOCs), can participate in new particle formation (NPF) throught interacting with sulfuric acid (SA) and organic acids. In this study, we investigated the molecular interactions of formamide (FA), acetamide (AA), N-methylformamide (MF), propanamide (PA), N-methylacetamide (MA), and N,N-dimethylformamide (DMF) with SA, acetic acid (HAC), propanoic acid (PAC), oxalic acid (OA), and malonic acid (MOA). Global minimum of clusters were obtained through the association of the artificial bee colony (ABC) algorithm and density functional theory (DFT) calculations. The conformational analysis, thermochemical analysis, frequency analysis, and topological analysis were conducted to determine the interactions of hydrogen-bonded molecular clusters. The heterodimers formed a hepta or octa membered ring through four different types of hydrogen bonds, and the strength of the bonds are ranked in the following order: SOH•••O > COH•••O > NH•••O > CH•••O. We also evaluated the stability of the clusters and found that the stabilization effect of amides with SA is weaker than that of amines with SA but stronger than that of ammonia (NH₃) with SA in the dimer formation of nucleation process. Additionally, the nucleation capacity of SA with amides is greater than that of organic acids with amides.

Halogen bonds and other noncovalent interactions in the crystal structures of trans-1,2-diiodo alkenes: an ab initio and QTAIM study

A series of interatomic interactions interpretable as halogen bonds involving I…I, I…O, and I…C(π), as well as the noncovalent interactions I…H and O…O, were observed in the crystal structures of trans-1,2-diiodoolefins dimers according to ab initio calculations and the quantum theory of "atoms in molecules" (QTAIM) method. The interplay between each type of halogen bond and other noncovalent interactions was studied systematically in terms of bond length, electrostatic potential, and interaction energy, which are calculated via ab initio methods at the B3LYP-D3/6-311++G(d,p) and B3LYP-D3/def2-TZVP levels of theory. Characteristics and nature of the halogen bonds and other noncovalent interactions, including the topological properties of the electron density, the charge transfer, and their strengthening or weakening, were analyzed by means of both QTAIM and "natural bond order" (NBO). These computational methods provide additional insight into observed intermolecular interactions and are utilized to explain the differences seen in the crystal structures. Graphical abstract The contour map presents the regions of electronic concentration and depletion along each bond in one dimer. The blue points denote the BCPs. The blue lines denote positive Laplacian of electron density, which indicate the ionic interactions, van der Waals or intermolecular interactions, and the red lines denote negative Laplacian of electron density which indicate the covalent bonds.

A molecular understanding of the interaction of typical aromatic acids with common aerosol nucleation precursors and their atmospheric implications

Aromatic acids, which are generated from numerous anthropogenic emissions and secondary transformations, have been considered to play a crucial role in new particle formation. In this study, we performed theoretical calculations at the PW91PW91/6-311++G(3df,3pd) level to investigate the interaction between typical aromatic acids namely benzoic acid (BA), phenylacetic acid (PAA), phthalic acid (PA), isophthalic acid (mPA), and terephthalic acid (PTA) and common atmospheric nucleation precursors namely sulfuric acid (SA), water (H2O), ammonia (NH3), methylamine (MA), dimethylamine (DMA), and trimethylamine (TMA). The geometric analysis, Gibbs free energy analysis, OH/NH-stretching vibrational frequency calculation, and atoms in molecules (AIM) analysis were conducted to determine the interactions in the complexes. The heterodimers formed a six to eight membered ring through four types of hydrogen bond, and the bond strength could be ranked in descending order: SO-H⋯O > O-H⋯O/N > N-H⋯O. The BA/PAA/mPA/PTA-SA complexes had the lowest Gibbs free energy values. PA was more likely to interact with NH3 or amines rather than SA due to an intra-molecular hydrogen bond. Additionally, the aromatic acids have similar ability to interact with SA and NH3 as monocarboxylic/dicarboxylic acid. The formation potential of the heterodimers from aromatic acids with common nucleation precursors in ambient atmosphere was investigated.

Molecular Understanding of Solvents and Glycitein Interaction during Extraction

Hydrogen bonding interaction plays a crucial role in liquid systems. Methanol, ethanol, and acetone are the most commonly used solvents to extract isoflavones from soybeans. The structural and electronic properties of the molecular clusters of naturally occurring glycitein with solvents were investigated using the density functional theory method employing the B3LYP-D3/cc-pVTZ approach. The influence of the solvent was carried out by using the polarized continuum model (PCM). The geometry optimization, vibrational frequencies, and topological parameters have been assessed at the same level of theory. From the molecular structure and thermodynamic point of view, the most stable structures are formed by the interaction between the carbonyl group of glycitein and MeOH or EtOH. For acetone-glycitein, the strongest interaction is formed by the interaction of the hydroxyl group of glycitein with the carbonyl group of acetone. All the hydrogen bonds in the MeOH/EtOH/acetone-glycitein complexes are closed-shell interactions. This study can help increase the efficiency of extraction.

Microhydration of protonated 5-hydroxyindole revealed by infrared spectroscopy

Controlled microsolvation of protonated aromatic biomolecules with water is fundamental to understand proton transfer reactions in aqueous environments. We measured infrared photodissociation (IRPD) spectra of mass-selected microhydrates of protonated 5-hydroxyindole (5HIH+-Wn, W = H2O, n = 1-3) in the OH and NH stretch ranges (2700-3800 cm-1), which are sensitive to the spectroscopic characteristics of interior solvation, water network formation, and proton transfer to solvent. Analysis of the IRPD spectra by dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ) reveals the coexistence of C3- and C4-protonated carbenium ions, 5HIH+(C3) and 5HIH+(C4), as well as the O-protonated oxonium ion, 5HIH+(O). Monohydrated 5HIH+-W clusters are formed by hydrogen-bonding (H-bonding) of the first water to the most acidic functional group, namely, the NH group in the case of 5HIH+(C3), the OH group for 5HIH+(C4), and the OH2 group for 5HIH+(O). The latter benefits from its twofold degeneracy and the outstandingly high binding energy of D0 ∼ 100 kJ mol-1. Larger 5HIH+-W2/3 clusters preferably grow (i) by H-bonding of the second water to the remaining vacant functional group and and/or (ii) by formation of W2 water chains at the respective most acidic functional group. Our IRPD spectra of 5HIH+-Wn do not indicate any proton transfer to the solvent up to n = 3, in line with the proton affinities of 5HI and Wn. Comparison of 5HIH+-Wn to neutral 5HI-W and cationic 5HI+-Wn clusters elucidates the impact of different charge states on the topology of the initial solvation shell. Furthermore, to access the influence of the size of the arene ion and a second functional group, we draw a comparison to microhydration of protonated phenol.

Molecular interaction between MeOH and genistein during soy extraction

Genistein has received great attention due to its possible anti-oxidant properties. The interaction between genistein and the extraction solvent helps in understanding the extraction efficiency. Hydrogen bonding plays a crucial role in liquid systems. Density functional theory quantum chemical computations in both gas phase and solution were performed to investigate the molecular interaction between genistein and methanol. All the resulting complexes (MeOH : genistein = 1 : 1, 2 : 1, 3 : 1, 6 : 1) were studied using the B3LYP-D3 computational level and the cc-pVTZ basis set. Binding energies demonstrate that more MeOH molecules surrounding genistein could stabilize the system more. Geometry optimizations show that there are strong O–H⋯O interactions between MeOH and genistein. The electron density and the corresponding Laplacian of charge density at bond critical points were also calculated using AIM theory, and the results are in line with the structural and energetic analysis of the studied system. Moreover, energy decomposition analysis shows that the exchange energy term has the largest contribution to the attraction interaction energy as compared with other energy terms. Meanwhile, this study shows that the MeOH–genistein system is more stable under basic conditions. This study could help increase the efficiency of extraction.

The interaction between genistein and extraction solvent helps in understanding the extraction efficiency.

The role of nitric acid in atmospheric new particle formation

Nitric acid, an air pollutant with strong acidity and oxidizability, can be found in considerable quantities in the gas and aerosol phase. Understanding the role of nitric acid in atmospheric new particle formation is essential to study the complicated nucleation mechanism. Using density functional theory combined with the Atmospheric Clusters Dynamic Code (ACDC), the role of nitric acid in the formation of new particles has been investigated under different atmospheric conditions (different precursor concentrations and temperatures). The results show that nitric acid can form clusters with sulfuric acid and ammonia by hydrogen bond or even proton-transfer interactions. The concentrations of clusters involving nitric acid can be comparable with those of sulfuric acid-ammonia-based clusters, considering the thermodynamic stability combined with the realistic atmospheric concentrations of precursors. Within the atmospheric concentration range, nitric acid can enhance the formation rates of sulfuric acid-ammonia clusters, especially at low temperature, low sulfuric acid concentration and high ammonia concentration. In addition, the new particle formation mechanism indicates that nitric acid can contribute to the cluster formation and the role of nitric acid in the cluster formation pathway is as a "bridge" connecting the smaller and larger clusters.

Gas-phase hydration of glyoxylic acid: Kinetics and atmospheric implications

Oxocarboxylic acids are one of the most important organic species found in secondary organic aerosols and can be detected in diverse environments. But the hydration of oxocarboxylic acids in the atmosphere has still not been fully understood. Neglecting the hydration of oxocarboxylic acids in atmospheric models may be one of the most important reasons for the significant discrepancies between field measurements and abundance predictions of atmospheric models for oxocarboxylic acids. In the present paper, glyoxylic acid, as the most abundant oxocarboxylic acids in the atmosphere, has been selected as an example to study whether the hydration process can occur in the atmosphere and what the kinetic process of hydration is. The gas-phase hydration of glyoxylic acid to form the corresponding geminal diol and those catalyzed by atmospheric common substances (water, sulfuric acid and ammonia) have been investigated at the CCSD(T)-F12/cc-pVDZ-F12//M06-2X/6-311++G(3df,3pd) level of theory. The contour map of electron density difference of transition states have been further analyzed. It is indicated that these atmospheric common substances can all catalyze on the hydration to some extent and sulfuric acid is the most effective reducing the Gibbs free energy of activation to 9.48 kcal/mol. The effective rate constants combining the overall rate constants and concentrations of the corresponding catalysts have shown that water and sulfuric acid are both important catalysts and the catalysis of sulfuric acid is the most effective for the gas-phase hydration of glyoxylic acid. This catalyzed processes are potentially effective in coastal regions and polluted regions.

Hydrogen bond docking site competition in methyl esters

The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm^-1)>TFE-MF (93cm^-1)>TFE-MTFA (44cm^-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol^-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF₃ substitution on MTFA, while the replacement of an H atom with a CH₃ group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.

Contribution of methane sulfonic acid to new particle formation in the atmosphere

Methane sulfonic acid (MSA) is present in substantial concentrations in the gas phase over oceans and coastal regions. We present an investigation into the contribution of MSA to new particle formation with the common atmospheric aerosol nucleation precursors including MSA, methanol, formic acid, acetone, dimethylether, formaldehyde, methyl formate, by making use a quantum chemical approach. Density functional theory calculations indicate that these bimolecular complexes are characterized by the presence of strong inter-molecular hydrogen bonds (SOH⋯O) with large binding energies and thermodynamic equilibrium constants. Topological analysis employing quantum theory of atoms in molecules shows that the charge density of the SOH⋯O hydrogen bonds of the MSA complexes falls in the range of hydrogen bonding criteria, but the Laplacian at bond critical points exceeds the range, which is due to the strong hydrogen bonding interactions. In all the studied complexes, the electrostatic interactions are found to be the main attractive force by localized molecular orbital energy decomposition analysis. All these indicate the environmental fate of MSA could play the role of nucleation centers in new particle formation. The effect of the atmospheric heights (0-12 km) was also considered. The Gibbs free energy of formation decreases with the increase of the atmospheric height owing to the decrease of the atmospheric temperature and pressure. The calculated Gibbs free energies of formation within the atmospheric temperature and pressure range could help to understand the atmospheric pollution.

Atmospheric implication of the hydrogen bonding interaction in hydrated clusters of HONO and dimethylamine in the nighttime

In this study, the stability of clusters formed by the trans- and cis-isomers of nitrous acid (HONO) with dimethylamine (DMA) and water has been characterized by density functional theory. The large red shifts of the OH-stretching transitions of both HONO isomers in the clusters indicate the formation of strong hydrogen bonds. At standard temperature and pressure, H₂O (acceptor) binds to HONO (donor) with binding energies of -25.0 to -24.6 kJ mol^-1, less stable than those of DMA (acceptor) with HONO (donor) (-50.5 to -45.3 kJ mol^-1). Our findings indicate that hydration enhances proton transfer from HONO to DMA, and consequently increases the interaction strength (binding energies = -67.8 to -78.6 kJ mol^-1). The topological and generalized Kohn-Sham energy decomposition confirms strong hydrogen bond interactions. The clustering of HONO with DMA in the atmosphere is negligible as compared to the important H₂SO₄-DMA clusters.

Basis set convergence of the binding energies of strongly hydrogen-bonded atmospheric clusters

We present the first binding energy benchmark set at the CBS limit of strongly hydrogen bonded atmospheric molecular clusters.

Theoretical investigation of gas-phase molecular complex formation between 2-hydroxy thiophenol and a water molecule

A systematic study of the interaction energies and hydrogen bonding interaction of a gas-phase molecular complex between 2-hydroxy thiophenol and a water molecule.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

Hydrogen bonding in cyclic complexes of carboxylic acid–sulfuric acid and their atmospheric implications

Carboxylic acids form cyclic ring structures with sulfuric acid and they could potentially be important in new particle formation.