Benzene Forms Hydrogen Bonds with Water

Effect of microhydration on the aromatic charge resonance interaction: the case of the pyrrole dimer cation

Charge resonance (CR) interactions between aromatic molecules are amongst the strongest intermolecular forces and responsible for many phenomena in chemistry and biology. Microhydration of an aromatic radical dimer cation allows investigation of the strong effects of stepwise solvation on the charge distribution and strength of the CR. We characterise herein the microhydration process of the pyrrole dimer cation (Py2+), a prototypical aromatic homodimer with a strong CR. The NH and OH stretch vibrations (νNH/OH) of mass-selected bare and colder Ar-tagged hydrated clusters of Py2+, Py2+(H2O)nArm (n ≤ 3, m ≤ 1), recorded by infrared photodissociation (IRPD) spectroscopy provide detailed insight into the preferred cluster growth and strengths of the various intermolecular interactions by comparison to dispersion-corrected density functional theory calculations. The analysis of systematic frequency shifts, structural parameters, binding energies, and charge distributions allows for a quantitative evaluation of the drastic effects of stepwise hydration on the strength and symmetry of the aromatic CR, the strengths of the various hydrogen bonds (H-bonds), and the competition between slightly noncooperative interior ion hydration and strongly cooperative formation of a H-bonded solvent network. The most stable Py2+H2O structure exhibits a strong NH⋯O ionic H-bond of H2O to the antiparallel stacked Py2+(a) core, thereby breaking the symmetry of the CR. Py2+(H2O)2 prefers a highly symmetric C2h structure with two equivalent NH⋯O H-bonds of Py2+(a) and an optimised CR. Starting from n = 3, clusters with a parallel configuration, Py2+(p), are more stable than those with Py2+(a), further highlighting the strong impact of (micro-)solvation on the structural motif of the aromatic CR. The spectral and computational data demonstrate a linear correlation of νNH of the free Py unit with its partial charge, illustrating that IR spectroscopy is a powerful tool for probing the charge distribution in aromatic CR cluster cations. Comparison of Py2+(H2O)n with neutral Py2(H2O)n and Py+(H2O)n reveals the impact of the magnitude of positive charge and the number of acidic proton donors on the structure of the microhydration shell and strength of the various competing intermolecular bonds.

Influence of Side Chain-Backbone Interactions and Explicit Hydration on Characteristic Aromatic Raman Fingerprints as Analysed in Tripeptides Gly-Xxx-Gly (Xxx = Phe, Tyr, Trp)

Because of the involvement of π-electron cyclic constituents in their side chains, the so-called aromatic residues give rise to a number of strong, narrow, and well-resolved lines spread over the middle wavenumber (1800-600 cm-1) region of the Raman spectra of peptides and proteins. The number of characteristic aromatic markers increases with the structural complexity (Phe → Tyr → Trp), herein referred to as (Fi = 1, …, 6) in Phe, (Yi = 1, …, 7) in Tyr, and (Wi = 1, …, 8) in Trp. Herein, we undertake an overview of these markers through the analysis of a representative data base gathered from the most structurally simple tripeptides, Gly-Xxx-Gly (where Xxx = Phe, Tyr, Trp). In this framework, off-resonance Raman spectra obtained from the aqueous samples of these tripeptides were jointly used with the structural and vibrational data collected from the density functional theory (DFT) calculations using the M062X hybrid functional and 6-311++G(d,p) atomic basis set. The conformation dependence of aromatic Raman markers was explored upon a representative set of 75 conformers, having five different backbone secondary structures (i.e., β-strand, polyproline-II, helix, classic, and inverse γ-turn), and plausible side chain rotamers. The hydration effects were considered upon using both implicit (polarizable solvent continuum) and explicit (minimal number of 5-7 water molecules) models. Raman spectra were calculated through a multiconformational approach based on the thermal (Boltzmann) average of the spectra arising from all calculated conformers. A subsequent discussion highlights the conformational landscape of conformers and the wavenumber dispersion of aromatic Raman markers. In particular, a new interpretation was proposed for the characteristic Raman doublets arising from Tyr (~850-830 cm-1) and Trp (~1360-1340 cm-1), definitely excluding the previously suggested Fermi-resonance-based assignment of these markers through the consideration of the interactions between the aromatic side chain and its adjacent peptide bonds.

Complex Dance of Molecules in the Sky: Choreography of Intermolecular Structure and Dynamics in the Cyclopentene-CO2-H2O Hetero Ternary Cluster

This study delves into driving forces behind the formation of a hetero ternary cluster consisting of volatile organic compounds from industrial or combustion sources, specifically cyclopentene, alongside greenhouse gases like carbon dioxide, and water vapor. While substantial progress has been made in understanding binary complexes, the structural intricacies of hetero ternary clusters remain largely uncharted. Our research characterized the cyclopentene-CO2-H2O hetero ternary cluster utilizing Fourier transform microwave spectroscopy. The observed isomer in the pulsed jet has CO2 and H2O aligning above the cyclopentene ring, with water undergoing an internal rotation approximately about its C2 symmetry axis. Theoretical analyses support these observations, identifying an O-H⋅⋅⋅π hydrogen bond and a secondary C⋅⋅⋅O tetrel bond within this cluster. This study marks a critical step towards comprehending the molecular dynamics and interactions of VOCs, greenhouse gases, and water in the atmosphere, paving the way for further investigations into their roles in climate dynamics and air quality.

Relationships between conformational and vibrational features of tryptophan characteristic Raman markers

Tryptophan (Trp) residue provides characteristic vibrational markers to the middle wavenumber spectral region of the Raman spectra recorded from peptides and proteins. In this report, we were particularly interested in eight Trp Raman markers, referred to as Wi (i = 1,…,8). All responsible for pronounced Raman lines, these markers originate from indole moiety, a bicyclic conjugated segment involved in the Trp structure. Numerous investigations have previously attempted to relate the variations observed in the spectral features of these markers to the environmental changes of Trp residues. To emphasize the most important points we can mention (i) the variations in the Raman profile of W4 (∼1360 cm-1) and W5 (∼1340 cm-1), frequently observed as a doublet with variable intensity ratio. These two markers were thought to result from a Fermi-resonance effect between certain planar and nonplanar modes; (ii) the changes observed in the wavenumbers and relative intensities of W4, W7 (∼880 cm-1) and W8 (∼760 cm-1) were supposed to be related to the accessibility of Trp to surrounding water molecules; and (iii) the wavenumber fluctuations of W3 (∼1550 cm-1), taken as a Trp side chain orientational marker. However, some ambiguities still exist regarding the interpretation of these markers, needing further clarification. Herein, upon a joint experimental and theoretical analysis based on a multiconformational approach, attention was paid to the relationships between structural and vibrational features of three indole-containing compounds with increasing structural complexity, i.e., skatole (3-methylindole), tryptophan, and tripeptide Gly-Trp-Gly. This study clearly shows that the existing assignments given to certain Trp Raman markers should be reconsidered, especially those based on the Fermi-resonance origin of W4-W5 (∼1360-1340 cm-1) doublet, as well as the purely environmental dependence of W7 and W8 markers.

Catalyst-free selective oxidation of C(sp3)-H bonds in toluene on water

The anisotropic water interfaces provide an environment to drive various chemical reactions not seen in bulk solutions. However, catalytic reactions by the aqueous interfaces are still in their infancy, with the emphasis being on the reaction rate acceleration on water. Here, we report that the oil-water interface activates and oxidizes C(sp3)-H bonds in toluene, yielding benzaldehyde with high selectivity (>99%) and conversion (>99%) under mild, catalyst-free conditions. Collision at the interface between oil-dissolved toluene and hydroxyl radicals spontaneously generated near the water-side interfaces is responsible for the unexpectedly high selectivity. Protrusion of free OH groups from interfacial water destabilizes the transition state of the OH-addition by forming π-hydrogen bonds with toluene, while the H-abstraction remains unchanged to effectively activate C(sp3)-H bonds. Moreover, the exposed free OH groups form hydrogen bonds with the produced benzaldehyde, suppressing it from being overoxidized. Our investigation shows that the oil-water interface has considerable promise for chemoselective redox reactions on water without any catalysts.

Internal Energy Dependence of the Pyrrole Dimer Cation Structures Formed in a Supersonic Plasma Expansion: Charge-Resonance and Hydrogen-Bonded Isomers

The structures of the pyrrole dimer cation (Py2+) formed in an electron-ionization-driven supersonic plasma expansion of Py seeded in Ar or N2 are probed as a function of its internal energy by infrared photodissociation (IRPD) spectroscopy in a tandem mass spectrometer. The IRPD spectra recorded in the CH and NH stretch ranges are analyzed by dispersion-corrected density functional theory (DFT) calculations at the B3LYP-D3/aug-cc-pVTZ level. The spectra of the cold Ar/N2-tagged Py2+ clusters, Py2+Ln (n = 1-5 for Ar, n = 1 for N2), indicate the exclusive formation of the most stable antiparallel π-stacked Py2+ structure under cold conditions, which is stabilized by charge-resonance interaction. The bare Py2+ dimers produced in the ion source have higher internal energy, and the observation of additional transitions in their IRPD spectra suggests a minor population of less stable hydrogen-bonded isomers composed of heterocyclic Py/Py+ structures formed after intramolecular H atom transfer and ring opening. These intermolecular isomers differ from the chemically bonded structures proposed earlier in the analysis of IRPD spectra of Py2+ generated by VUV ionization of neutral Pyn clusters.

Comparison of the Interaction and Structure of Lignin in Pure Systems and in Asphalt Media by Molecular Dynamics Simulations

Lignin is a class of organic aromatic polymers contributing to the rigidity and strength of plants and has been proposed as a modifier to improve asphalt performance on road pavement. However, contradicting experimental results on the lignin miscibility in asphalt were found from different studies, and lignin has been found to self-assemble in different solutions. Thus, investigating the interaction and microstructure of lignin in asphalt media in molecular detail is necessary. Molecular dynamics (MD) simulations using both the LAMMPS program with the OPLS-aa force field and the NAMD program with the CHARMM force field have been conducted on pure lignin (including lignin monomer, dimer, and polymer with 17 and 31 units) and their mixtures with model asphalt molecules at different temperatures. Consistent results were observed from both programs and force fields in terms of density, hydrogen bonds, diffusion coefficient, radius of gyration, and radial distribution function. Glass transition was observed in the pure lignin systems based on density and diffusion coefficient calculations at different temperatures. Lignin can form intramolecular hydrogen bonds and intermolecular hydrogen bonds with other lignin and 1,7-dimethylnapthalene in the asphalt mixture, which has dependence on temperature and lignin chain length. Correlating the lignin size and chain length using the power-law relationship showed that lignin polymers in pure systems are in quasi-relaxed structures at different temperatures; lignin molecules stay in quasi-relaxed structures in asphalt mixtures at high temperatures but in collapsed structures at low temperatures. Implementing lignin monomer, dimer, and polymer into the model asphalt mixture can improve its density. Although lignin in different chain lengths aggregates in asphalt, lignin can modify the packing between different components in asphalt media at different temperatures. The work suggests that temperature can significantly influence the miscibility of lignin polymer in asphalt and that lignin can function as both a modifier and a resin in asphalt.

Water-Induced Micro-Hydrophobic Effect Regulates Benzene Methylation in Zeolite

Water is a ubiquitous component in heterogeneous catalysis over zeolites and can significantly influence the catalyst performance. However, the detailed mechanism insights into zeolite-catalyzed reactions under microscale aqueous environment remain elusive. Here, using multiple dimensional solid-state NMR experiments coupled with ultrahigh magic angle spinning technique and theoretical simulations, we establish a fundamental understanding of the role of water in benzene methylation over ZSM-5 zeolite under water vapor conditions. We show that water competes with benzene for the active sites of zeolite and facilitates the bimolecular reaction mechanism. The growth of water clusters induces a micro-hydrophobic effect in zeolite pores, which reorients benzene molecules and drives their interactions with surface methoxy species (SMS) on zeolite. We identify the formation and evolution of active SMS-Benzene complexes in a microscale aqueous environment and demonstrate that their accumulation in zeolite pores boosts benzene conversion and methylation.

The Field of Main Group Lewis Acids and Lewis Superacids: Important Basics and Recent Developments

New developments in the field of Lewis acidity are highlighted, with the focus of novel Lewis acids and Lewis superacids of group 2, 13, 14, and 15 elements. Several important basics, illustrated by modern examples (classification of Donor-Acceptor (DA) complexes, amphoteric nature of any compound in terms of DA interactions, reorganization energies of main group Lewis acids and the role of the energies of frontier orbitals) are presented and discussed. It is emphasized that the Lewis acidity phenomena are general and play vital role in different areas of chemistry: from weak "atomophilic" interactions to the complexes of Lewis superacids.

In vitro Modified Release Studies on Melatoninergic Fluorinated Phenylalkylamides: Circumventing their Lipophilicity for Oral Administration

INTRODUCTION

In an attempt to circumvent the lipophilicity burden for the oral administration of new potent synthetic melatoninergic fluorine-substituted methoxyphenylalkyl amides, we conducted in vitro modified release studies using carefully selected matrix tablets' biopolymeric materials in different ratios.

METHODS

In particular, we sought to attain release profiles of these analogues similar to that of the parent compound, the chronobiotic hormone Melatonin (MLT), and also of the commercially available drug, Circadin®.

RESULTS

It was found that some of these systems, albeit being more lipophilic than MLT, mimic the in vitro release patterns of melatonin and Circadin®.

CONCLUSION

Moreover, a number of these derivatives were proven suitable for dealing with sleep onset problems, whilst others for dealing with combined sleep onset/sleep maintenance dysfunctions.

Imaging of Single Molecular Behaviors Under Bifurcated Three-Centered Hydrogen Bonding

The mechanism for interaction and bonding of single guest molecules with active sites fundamentally determines the sorption and subsequent catalytic processes occurring in host zeolitic frameworks. However, no real-space studies on these significant issues have been reported thus far, since atomically visualizing guest molecules and recognizing single Al T-sites in zeolites remain challenging. Here, we atomically resolved single thiophene probes interacting with acid T-sites in the ZSM-5 framework to study the bonding behaviors between them. The synergy of bifurcated three-centered hydrogen bonds and van der Waals interactions can "freeze" the near-horizontal thiophene and make it stable enough to be imaged. By combining the imaging results with simulations, direct atomic observations enabled us to precisely locate the single Al T-sites in individual straight channels. Then, we statistically found that the thiophene bonding probability of the T11 site is 15 times higher than that of the T6 site. For different acid T-sites, the variation in the interaction synergy changes the inner angle of the host-guest O-H⋅⋅⋅S hydrogen bond, thereby affecting the stability of the near-horizontal thiophene and leading to considerable bonding inhomogeneities.

Mixture Adsorption in Nanoporous Zeolite and at Its External Surface: In-Pore and Surface Selectivity

Using toluene, ethylene, and water as gas compounds with different representative molecular interactions, we perform atom-scale simulations for their mixtures to investigate the selectivity of the core nanoporosity and external surface in a prototypical zeolite. As expected, the overall behavior suggests that increasing the pressure of a given component promotes the desorption of the coadsorbing species. However, for water-toluene mixtures, we identify that the pseudohydrogen bonding between water and toluene leads to beneficial coadsorption as toluene adsorption in the low-pressure range promotes water adsorption. Moreover, when the zeolite is completely filled with water, toluene adsorption does not occur due to steric repulsion, and ethylene shows oversolubility as the amount of ethylene per water molecule is significantly larger than in bulk water. The underlying oversolubility mechanism is found to be due to localized ethylene adsorption in the density minima arising from the layering of water in nanoconfinement. Despite these specific effects, the relatively weak coadsorption effects in the zeolite nanoporosity, which are found to be reasonably captured using the ideal adsorbed solution theory, arise from the fact that adsorption of these gases having different molecular sizes occurs in distinct pore regions (channel type, channel intersection). Finally, in contrast to confinement in the nanoporosity, mixture adsorption at the external surface does not show coadsorption effects as it mostly follows the Henry regime. These results show that selectivity is mostly governed by the confinement effects as the external surface leads to a selectivity loss.

Strong structuring arising from weak cooperative O-H···π and C-H···O hydrogen bonding in benzene-methanol solution

Weak hydrogen bonds, such as O-H···π and C-H···O, are thought to direct biochemical assembly, molecular recognition, and chemical selectivity but are seldom observed in solution. We have used neutron diffraction combined with H/D isotopic substitution to obtain a detailed spatial and orientational picture of the structure of benzene-methanol mixtures. Our analysis reveals that methanol fully solvates and surrounds each benzene molecule. The expected O-H···π interaction is highly localised and directional, with the methanol hydroxyl bond aligned normal to the aromatic plane and the hydrogen at a distance of 2.30 Å from the ring centroid. Simultaneously, the tendency of methanol to form chain and cyclic motifs in the bulk liquid is manifest in a highly templated solvation structure in the plane of the ring. The methanol molecules surround the benzene so that the O-H bonds are coplanar with the aromatic ring while the oxygens interact with C-H groups through simultaneous bifurcated hydrogen bonds. This demonstrates that weak hydrogen bonding can modulate existing stronger interactions to give rise to highly ordered cooperative structural motifs that persist in the liquid phase.

Probing a Hydrogen-π Interaction Involving a Trapped Water Molecule in the Solid State

The detection and characterization of trapped water molecules in chemical entities and biomacromolecules remains a challenging task for solid materials. We herein present proton-detected solid-state Nuclear Magnetic Resonance (NMR) experiments at 100 kHz magic-angle spinning and at high static magnetic-field strengths (28.2 T) enabling the detection of a single water molecule fixed in the calix[4]arene cavity of a lanthanide complex by a combination of three types of non-covalent interactions. The water proton resonances are detected at a chemical-shift value close to zero ppm, which we further confirm by quantum-chemical calculations. Density Functional Theory calculations pinpoint to the sensitivity of the proton chemical-shift value for hydrogen-π interactions. Our study highlights how proton-detected solid-state NMR is turning into the method-of-choice in probing weak non-covalent interactions driving a whole branch of molecular-recognition events in chemistry and biology.

Microhydration of the Pyrrole Cation (Py+) Revealed by IR Spectroscopy: Ionization-Induced Rearrangement of the Hydrogen-Bonded Network of Py+(H2O)2

Microhydration of heterocyclic aromatic molecules can be an appropriate fundamental model to shed light on intermolecular interactions and functions of macromolecules and biomolecules. We characterize herein the microhydration process of the pyrrole cation (Py⁺) by infrared photodissociation (IRPD) spectroscopy and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). Analysis of IRPD spectra of mass-selected Py⁺(H₂O)₂ and its cold Ar-tagged cluster in the NH and OH stretch range combined with geometric parameters of intermolecular structures, binding energies, and natural atomic charge distribution provides a clear picture of the growth of the hydration shell and cooperativity effects. Py⁺(H₂O)₂ is formed by stepwise hydration of the acidic NH group of Py⁺ by a hydrogen-bonded (H₂O)₂ chain with NH···OH···OH configuration. In this linear H-bonded hydration chain, strong cooperativity, mainly arising from the positive charge, strengthens both the NH···O and OH···O H-bonds with respect to those of Py⁺H₂O and (H₂O)₂, respectively. The linear chain structure of the Py⁺(H₂O)₂ cation is discussed in terms of the ionization-induced rearrangement of the hydration shell of the neutral Py(H₂O)₂ global minimum characterized by the so-called "σ-π bridge structure" featuring a cyclic NH···OH···OH···π H-bonded network. Emission of the π electron from Py by ionization generates a repulsive interaction between the positive π site of Py⁺ and the π-bonded OH hydrogen of (H₂O)₂, thereby breaking this OH···π hydrogen bond and driving the hydration structure toward the linear chain motif of the global minimum on the cation potential.

Molecular Structure, Electronic Properties, Reactivity (ELF, LOL, and Fukui), and NCI-RDG Studies of the Binary Mixture of Water and Essential Oil of Phlomis bruguieri

Essential oils are volatile oil-like liquids with a characteristic strong smell and taste. They are formed in plants and are then extracted. Essential oils have extremely strong physiological and pharmacological properties, which are used in the medicine, cosmetics, and food industries. In this study, the molecules caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene, which are the molecules with the highest contents in the essential oil of the plant mentioned in the title, were selected and theoretical calculations describing their interactions with water were performed. Because oil-water mixtures are very important in biology and industry and are ubiquitous in nature, quantum chemical calculations for binary mixtures of water with caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene were performed using the density functional theory (DFT)/B3LYP method with a basis of 6-31 G (d, p). Molecular structures, HOMO-LUMO energies, electronic properties, reactivity (ELF, LOL, and Fukui), and NCI-RDG and molecular electrostatic potential (MEP) on surfaces of the main components of Phlomis bruguieri Desf. essential oil were calculated and described.

Stepwise hydrations of anhydride tuned by hydrogen bonds: rotational study on maleic anhydride-(H2O)1-3

The rotational spectra of maleic anhydride-(H₂O)_1-3 have been investigated for the first time by using pulsed jet Fourier transform microwave spectroscopy with complementary computational analyses. The experimental evidence points out that water tends to self-aggregate with hydrogen bonds and form homodromic cycles. Differences in bond lengths and charge distribution between the two carbonyl sites have been observed upon stepwise hydrations, which might further introduce a selectivity on the nucleophilic attack sites of hydrolysis. This study provides an important insight into the incipient solvation process (microsolvation) of maleic anhydride in water by understanding the cooperation and rearrangement of intermolecular hydrogen bonds in its stepwise hydrates.

Competition between In-Plane vs Above-Plane Configurations of Water with Aromatic Molecules: Non-Covalent Interactions in 1,4-Naphthoquinone-(H2O)1-3 Complexes

Non-covalent interactions between aromatic molecules and water are fundamental in many chemical and biological processes, and their accurate description is essential to understand molecular relative configurations. Here we present the rotational spectroscopy study of the water complexes of the polycyclic aromatic hydrocarbon 1,4-naphthoquinone (1,4-NQ). In 1,4-NQ-(H₂O)_1,2, water molecules bind through O-H···O and C-H···O hydrogen bonds and are located on the plane of 1,4-NQ. For 1,4-NQ-(H₂O)₃, in-plane and above-plane water configurations are observed exhibiting O-H···O, C-H···O, and lone pair···π-hole interactions. The observation of different water arrangements for 1,4-NQ-(H₂O)₃ allows benchmarking theoretical methods and shows that they have great difficulty in predicting energy orderings due to the strong competition of C-H···O binding with π and π-hole interactions. This study provides important insight into water interactions with aromatic systems and the challenges in their modeling.

Thermodynamics of π–π Interactions of Benzene and Phenol in Water

The π–π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π–π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy–entropy compensation. Our comprehensive computational study of the solvation effect on π–π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.

Transition Metal Catalysis Controlled by Hydrogen Bonding in the Second Coordination Sphere

Transition metal catalysis is of utmost importance for the development of sustainable processes in academia and industry. The activity and selectivity of metal complexes are typically the result of the interplay between ligand and metal properties. As the ligand can be chemically altered, a large research focus has been on ligand development. More recently, it has been recognized that further control over activity and selectivity can be achieved by using the "second coordination sphere", which can be seen as the region beyond the direct coordination sphere of the metal center. Hydrogen bonds appear to be very useful interactions in this context as they typically have sufficient strength and directionality to exert control of the second coordination sphere, yet hydrogen bonds are typically very dynamic, allowing fast turnover. In this review we have highlighted several key features of hydrogen bonding interactions and have summarized the use of hydrogen bonding to program the second coordination sphere. Such control can be achieved by bridging two ligands that are coordinated to a metal center to effectively lead to supramolecular bidentate ligands. In addition, hydrogen bonding can be used to preorganize a substrate that is coordinated to the metal center. Both strategies lead to catalysts with superior properties in a variety of metal catalyzed transformations, including (asymmetric) hydrogenation, hydroformylation, C-H activation, oxidation, radical-type transformations, and photochemical reactions.

Conformations and structures of 1,4-pentadien-3-ol and its water complex characterized by rotational spectroscopy

The 1,4-pentadien-3-ol and its monohydrate have been characterized by microwave spectroscopy in combination with theoretical computations. Experiments and ab initio calculations revealed that the 1,4-pentadien-3-ol monomer prefers a configuration with one vinyl being syn to the hydroxyl oxygen and the hydroxyl hydrogen toward the skew arranged vinyl, which therefore makes possible simultaneous CH···O and OH···π interactions. The observed monohydrate corresponds to the global minimum predicted theoretically, which is stabilized through a primary OH···O_w hydrogen bond together with a much weaker O_wH···π hydrogen bond. The NCI analyses, NBO calculation and SAPT method were applied to further elucidate the characteristics of hydrogen bonds in the 1,4-pentadien-3-ol···water complex.

Noncovalently bound molecular complexes beyond diatom–diatom systems: full-dimensional, fully coupled quantum calculations of rovibrational states

The methodological advances made in recent years have significantly extended the range and dimensionality of noncovalently bound molecular complexes for which full-dimensional quantum calculations of their rovibrational states are feasible.

Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

Abstract:

X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

Isotope Effects on the Vaporization of Organic Compounds from an Aqueous Solution-Insight from Experiment and Computations

An isotope fractionation analysis of organic groundwater pollutants can assess the remediation at contaminated sites yet needs to consider physical processes as potentially confounding factors. This study explores the predictability of water–air partitioning isotope effects from experiments and computational predictions for benzene and trimethylamine (both H-bond acceptors) as well as chloroform (H-bond donor). A small, but significant, isotope fractionation of different direction and magnitude was measured with ε = −0.12‰ ± 0.07‰ (benzene), ε_C = 0.49‰ ± 0.23‰ (triethylamine), and ε_H = 1.79‰ ± 0.54‰ (chloroform) demonstrating that effects do not correlate with expected hydrogen-bond functionalities. Computations revealed that the overall isotope effect arises from contributions of different nature and extent: a weakening of intramolecular vibrations in the condensed phase plus additional vibrational modes from a complexation with surrounding water molecules. Subtle changes in benzene contrast with a stronger coupling between intra- and intermolecular modes in the chloroform–water system and a very local vibrational response with few atoms involved in a specific mode of triethylamine. An energy decomposition analysis revealed that each system was affected differently by electrostatics and dispersion, where dispersion was dominant for benzene and electrostatics dominated for chloroform and triethylamine. Interestingly, overall stabilization patterns in all studied systems originated from contributions of dispersion rather than other energy terms.

Biophysical Evaluation and In Vitro Controlled Release of Two Isomeric Adamantane Phenylalkylamines with Antiproliferative/Anticancer and Analgesic Activity

The aqueous dissolution profile of the isomeric synthetic adamantane phenylalkylamine hydrochlorides I and II was probed. These adducts have shown significant antiproliferative/anticancer activity associated with an analgesic profile against neuropathic pain. They are both devoid of toxic effects and show appreciable enzymatic human plasma stability. The structures of these two compounds have been elucidated using 2D NMR experiments, which were used to study their predominant conformations. Compound II’s scaffold appeared more flexible, as shown by the NOE spatial interactions between the alkyl bridge chain, the aromatic rings, and the adamantane nucleus. Conversely, compound I appeared very rigid, as it did not share significant NOEs between the aforementioned structural segments. MD simulations confirmed the NOE results. The aqueous dissolution profile of both molecules fits well with their minimum energy conformers’ features, which stem from the NOE data; this was nicely demonstrated, especially in the case of compound II.

An infrared spectroscopic study of trifluoromethoxybenzene⋯methanol complexes formed in superfluid helium nanodroplets

We have studied the intermolecular complex formation between trifluoromethoxybenzene and methanol (CD₃OD) in superfluid helium droplets by infrared spectroscopy in the spectral range of 2630-2730 cm^-1, covering the O-D stretches of methanol-d₄ (CD₃OD). The cluster size associated with the observed bands is deduced from the variation of infrared intensity of a particular band with the partial pressures of trifluoromethoxybenzene and methanol. Quantum chemical calculations are performed at the MP2/6-311++G(d,p) level of theory to complement the experimental results. As a result, we have identified six different conformers of the trifluoromethoxybenzene⋯methanol intermolecular complex: three bound via O-H⋯O hydrogen bonds and the other three via O-H⋯π hydrogen bonds. Furthermore, to access the effect of fluorination on the methyl unit of anisole molecules, we compare the IR spectrum of trifluoromethoxybenzene (C₆H₅OCF₃)⋯methanol with our earlier reported spectrum of anisole (C₆H₅OCH₃)⋯methanol.

Beyond the Molecule: Intermolecular Forces from Gas Liquefaction to X-H⋅⋅⋅π Hydrogen Bonds

Interest toward molecule-molecule interactions developed during the first half of the 19th century with studies on gas liquefaction. In 1869, Andrews carried out the first accurate study on the effects of temperature and pressure on the behaviour of real gases, and in 1873, van der Waals formulated an equation capable of accounting for critical phenomena of each individual gas The nature of the intermolecular forces responsible for aggregation of gases was investigated in the early 20th century by Keesom and Debye (electrostatic interactions between dipoles) and by London (interaction between instantaneous dipoles, studied by quantum mechanics). The hydrogen bond theory, a particular case of dipolar interaction, originated in the 1920s in Berkeley in the institute directed by G. N. Lewis. Later it was made clear that hydrogen bonding is responsible for the aggregation of most biological systems, from proteins to nucleic acids. This Perspective describes the most significant steps through which the science of intermolecular interactions has progressed over the last two centuries, revisiting classical experiments and theoretical formulations, which led to the complex state of art of today.

Platinum Indolylphosphine Fluorido and Polyfluorido Complexes: An Interplay between Cyclometallation, Fluoride Migration, and Hydrogen Bonding

The reaction of [PtCl2 (COD)] (COD=1,5-cyclooctadiene) with diisopropyl-2-(3-methyl)indolylphosphine (iPr2 P(C9 H8 N)) led to the formation of the platinum(ii) chlorido complexes, cis-[PtCl2 {iPr2 P(C9 H8 N)}2 ] (1) and trans-[PtCl2 {iPr2 P(C9 H8 N)}2 ] (2). The cis-complex 1 reacted with NEt3 yielding the complex cis-[PtCl{κ2 -(P,N)-iPr2 P(C9 H7 N)}{iPr2 P(C9 H8 N)}] (3) bearing a cyclometalated κ2 -(P,N)-phosphine ligand, while the isomer 2 with a trans-configuration did not show any reactivity towards NEt3 . Treatment of 1 or 3 with (CH3 )4 NF (TMAF) resulted in the formation of the twofold cyclometalated complex cis-[Pt{κ2 -(P,N)-iPr2 P(C9 H7 N)}2 ] (4). The molecular structures of the complexes 1-4 were determined by single-crystal X-ray diffraction. The fluorido complex cis-[PtF{κ2 -(P,N)-iPr2 P(C9 H7 N)}{iPr2 P(C9 H8 N)}] ⋅ (HF)4 (5 ⋅ (HF)4 ) was formed when complex 4 was treated with different hydrogen fluoride sources. The Pt(ii) fluorido complex 5 ⋅ (HF)4 exhibits intramolecular hydrogen bonding in its outer coordination sphere between the fluorido ligand and the NH group of the 3-methylindolyl moiety. In contrast to its chlorido analogue 3, complex 5 ⋅ (HF)4 reacted with CO or the ynamide 1-(2-phenylethynyl)-2-pyrrolidinone to yield the complexes trans-[Pt(CO){κ2 -(P,C)-iPr2 P(C9 H7 NCO)}{iPr2 P(C9 H8 N)}][F(HF)4 ] (7) and a complex, which we suggest to be cis-[Pt{C=C(Ph)OCN(C3 H6 )}{κ2 -(P,N)-iPr2 P(C9 H7 N)}{iPr2 P(C9 H8 N)}][F(HF)4 ] (9), respectively. The structure of 9 was assigned on the basis of DFT calculations as well as NMR and IR data. Hydrogen bonding of HF and NH to fluoride was proven to be crucial for the existence of 7 and 9.

How Aromatic Fluorination Exchanges the Interaction Role of Pyridine with Carbonyl Compounds: The Formaldehyde Adduct

The rotational spectrum of the weakly bound complex pentafluoropyridine⋅⋅⋅formaldehyde has been investigated using Fourier transform microwave spectroscopy. From the analysis of the rotational parameters of the parent species and of the 13 C and 15 N isotopologues, the structural arrangement of the adduct has been unambiguously established. The full ring fluorination of pyridine has a dramatic effect on its binding properties: It alters the electron density distribution at the π-cloud of pyridine creating a π-hole and changing its electron donor-acceptor capabilities. In the complex, formaldehyde lies above the aromatic ring with one of the oxygen lone pairs, as conventionally envisaged, pointing toward its centre. This lone pair⋅⋅⋅π-hole interaction, reinforced by a weak C-H⋅⋅⋅N interaction, indicates an exchange of the electron-acceptor roles of both molecules when compared to the pyridine⋅⋅⋅formaldehyde adduct. Tunnelling doublets due to the internal rotation of formaldehyde have also been observed and analysed leading to a discussion on the competition between lone pair⋅⋅⋅π-hole and π⋅⋅⋅π stacking interactions.

Switching Aromatic Character by Complexation: π to π* Change Seen in Molecular Rotation Spectra

A dominating F···π*_aromatic interaction is found to govern the benzaldehyde···tetrafluoromethane complex, as revealed by this rotational spectroscopic investigation. Secondary F···π*_-C=O- and C σ*_CF4···π_aromatic interactions also contribute to the stability of the observed isomer. Narrow splittings have been observed in the rotational spectrum originating from a 3-fold internal rotation of CF₄ above the aromatic moiety, and a corresponding V₃ barrier was determined to be 1.572(14) kJ mol^-1. This is the first rotational spectroscopic evidence in the literature implying that the aromatic π* antibonding orbital can be activated not only by electron-withdrawing substituents but also by complexation partners containing atoms with high electronegativity, like CF₄. The results emphasize the partner molecules' role to modulate the π electron structure and show a change in the orbital character (π or π*) when participating in the formation of noncovalent interactions.

Do Docking Sites Persist Upon Fluorination? The Diadamantyl Ether-Aromatics Challenge for Rotational Spectroscopy and Theory

Fluorinated derivatives of biological molecules have proven to be highly efficient at modifying the biological activity of a given protein through changes in the stability and the kind of docking interactions. These interactions can be hindered or facilitated based on the hydrophilic/hydrophobic character of a particular protein region. Diadamantyl ether (C₂₀H₃₀O) possesses both kinds of docking sites, serving as a good template to model these important contacts with aromatic fluorinated counterparts. In this work, an experimental study on the structures of several complexes between diadamantyl ether and benzene as well as a series of fluorinated benzenes is reported to analyze the effect of H→F substitution on the interaction and structure of the resulting molecular clusters using rotational spectroscopy. All experimentally observed complexes are largely dominated by London dispersion interactions with the hydrogen‐terminated surface areas of diadamantyl ether. Already single substitution of one hydrogen atom with fluorine changes the preferred docking site of the complexes. However, the overall contributions of the different intermolecular interactions are similar for the different complexes, contrary to previous studies focusing on the difference in interactions using fluorinated and non‐fluorinated molecules.

Ruthenium Nanoparticles Intercalated in Montmorillonite (nano-Ru@MMT) Is Highly Efficient Catalyst for the Selective Hydrogenation of 2-Furaldehyde in Benign Aqueous Medium

Chemoselective hydrogenation of 2-furaldehyde to furfuryl alcohol using green solvents is an important research area to get eco-friendly fuels and fine chemicals. Herein, we report ruthenium nanoparticles (~1.8 nm) intercalated in montmorillonite as an efficient catalytic system, which can selectively hydrogenate 2-furaldehyde in a benign aqueous medium. The complete conversion was observed at 40 °C with 1 MPa H2, the selectivity of furfuryl alcohol being >99%, and turnover number 1165. After a catalytic run, the montmorillonite-supported ruthenium nanoparticles can be recycled and reused without losing their activity and selectivity.

Unravelling the microhydration frameworks of prototype PAH by infrared spectroscopy: naphthalene–(water)1–3

Microhydration structures of the prototypical PAH, naphthalene, are probed by IR spectroscopy in helium droplets. The sequential water addition produces an extended hydrogen-bonded hydration network bound via π hydrogen bond to the aromatic ring.

How does the composition of a PAH influence its microsolvation? A rotational spectroscopy study of the phenanthrene–water and phenanthridine–water clusters

The influence of a nitrogen atom in the backbone of a PAH was revealed by the hydrated clusters of phenanthrene and phenanthridine in a rotational spectroscopy study. Background image credit: NASA, ESA, and the Hubble Heritage Team (STScI/AURA) – ESA/Hubble Collaboration.

Unveiling the structural and energetic properties of thiazole-water complex by microwave spectroscopy and theoretical calculations

The structure and non-covalent bonding features of the complex of thiazole and water were studied by using supersonic jet Fourier transform microwave spectroscopy and theoretical calculations. One isomer was observed which corresponds to the global minimum of the complex predicted theoretically. The rotational spectra of 9 additional isotopologues, including 5 mono-substituted heavy atoms of thiazole (³⁴S, ¹³C and ¹⁵N), and 4 water isotopic species (H₂¹⁸O, DOH, HOD and D₂O), were also measured and analyzed. The experimental spectroscopic parameters were used to determine the structural parameters of the observed isomer. Theoretical analyses based on quantum theory of atoms in molecules and natural bond orbital revealed that the two moieties are linked by a N···H-O hydrogen bond. The total interaction energy of the complex is calculated to be -25.1 kJmol^-1 with electrostatics being the major term according to energy decomposition analysis.

Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects

During the last two decades, numerous observed data obtained by various physical techniques, also supported by molecular modeling approaches, have highlighted the structuring features of tripeptides, as well as their aggregation properties. Herein, we focus on the structural dynamics of four trimers, i.e., Gly-Gly-Gly, Gly-Ala-Gly, Ala-Ala-Ala and Ala-Phe-Ala, in an aqueous environment. Density functional theory calculations (DFT) were carried out to assess the stability of four types of secondary structures, i.e., β-strand, polyproline-II (pP-II), α-helix and γ-turn, of which the formation had been described in these tripeptides. Both implicit and explicit hydration effects were analyzed on the conformational and energetic features of trimers. It has been shown that the use of M062X functional (versus B3LYP) improve the stability of intramolecular H-bonds, especially in inverse γ-turn structures, as well as the energetic and conformational equilibrium in all tripeptides. Explicit hydration reflected by the presence of five water molecules around the backbone polar sites (NH₃⁺, N-H, CO and NH₂) considerably changes the conformational landscapes of the trimers. Characteristic intramolecular and intermolecular interactions evidenced by the calculations, were emphasized.

Rotational Spectroscopy Meets Quantum Chemistry for Analyzing Substituent Effects on Non-Covalent Interactions: The Case of the Trifluoroacetophenone-Water Complex

The most stable isomer of the 1:1 complex formed by 2,2,2-trifluoroacetophenone and water has been characterized by combining rotational spectroscopy in supersonic expansion and state-of-the-art quantum-chemical computations. In the observed isomer, water plays the double role of proton donor and acceptor, thus forming a seven-membered ring with 2,2,2-trifluoroacetophenone. Accurate intermolecular parameters featuring one classical O-H···O hydrogen bond and one weak C-H···O hydrogen bond have been determined by means of a semi-experimental approach for equilibrium structure. Furthermore, insights on the nature of the established non-covalent interactions have been unveiled by means of different bond analyses. The comparison with the analogous complex formed by acetophenone with water points out the remarkable role played by fluorine atoms in tuning non-covalent interactions.

NMR elucidation of nonproductive binding sites of lignin models with carbohydrate-binding module of cellobiohydrolase I

BACKGROUND

Highly efficient enzymatic saccharification of pretreated lignocellulose is a key step in achieving lignocellulosic biorefinery. Cellobiohydrolase I (Cel7A) secreted by Trichoderma reesei is an industrially used cellulase that possesses carbohydrate-binding module 1 (TrCBM1) at the C-terminal domain. The nonproductive binding of TrCBM1 to lignin significantly decreases the enzymatic saccharification efficiency and increases the cost of biomass conversion because of the additionally required enzymes. Understanding the interaction mechanism between lignin and TrCBM1 is essential for realizing a cost-effective biofuel production; however, the binding sites in lignin have not been clearly elucidated.

RESULTS

Three types of ¹³C-labeled β-O-4 lignin oligomer models were synthesized and characterized. The 2D ¹H-¹³C heteronuclear single-quantum correlation (HSQC) spectra of the ¹³C-labeled lignin models confirmed that the three types of the ¹³C labels were correctly incorporated in the (1) aromatic rings and β positions, (2) α positions, and (3) methoxy groups, respectively. The TrCBM1-binding sites in lignin were analyzed by observing NMR chemical shift perturbations (CSPs) using the synthetic ¹³C-labeled β-O-4 lignin oligomer models. Obvious CSPs were observed in signals from the aromatic regions in oligomers bound to TrCBM1, whereas perturbations in the signals from aliphatic regions and methoxy groups were insignificant. These findings indicated that hydrophobic interactions and π-π stacking were dominating factors in nonproductive binding. The synthetic lignin models have two configurations whose terminal units were differently aligned and donated C^(I) and C^(II). The C^(I) ring showed remarkable perturbation compared with the C^(II), which indicated that the binding of TrCBM1 was markedly affected by the configuration of the lignin models. The long-chain lignin models (degree of polymerization (DP) 4.16-4.70) clearly bound to TrCBM1. The interactions of TrCBM1 with the short-chain lignin models (DP 2.64-3.12) were insignificant, indicating that a DP greater than 4 was necessary for TrCBM1 binding.

CONCLUSION

The CSP analysis using ¹³C-labeled β-O-4 lignin oligomer models enabled the identification of the TrCBM1 binding sites in lignins at the atomic level. This specific interaction analysis will provide insights for new molecular designs of cellulase having a controlled affinity to cellulose and lignin for a cost-effective biorefinery process.

Binding Site Switch by Dispersion Interactions: Rotational Signatures of Fenchone-Phenol and Fenchone-Benzene Complexes

Non-covalent interactions between molecules determine molecular recognition and the outcome of chemical and biological processes. Characterising how non-covalent interactions influence binding preferences is of crucial importance in advancing our understanding of these events. Here, we analyse the interactions involved in smell and specifically the effect of changing the balance between hydrogen-bonding and dispersion interactions by examining the complexes of the common odorant fenchone with phenol and benzene, mimics of tyrosine and phenylalanine residues, respectively. Using rotational spectroscopy and quantum chemistry, two isomers of each complex have been identified. Our results show that the increased weight of dispersion interactions in these complexes changes the preferred binding site in fenchone and sets the basis for a better understanding of the effect of different residues in molecular recognition and binding events.

Local Vibrational Mode Analysis of π–Hole Interactions between Aryl Donors and Small Molecule Acceptors

11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different π –hole systems. Several factors have emerged which influence strength of the π –hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ π –hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the π –hole interaction strength, where electronegative aryl-substituents moderately increase π –hole interaction strength. N-aryl members significantly increase π –hole interaction strength, and anion acceptors bind more strongly with the π –hole compared to charge neutral acceptors (lone–pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase π –hole interaction strength, while hydrogen bonding between the π –hole acceptor/donor can significantly increase or decrease strength of the π –hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl π –hole interactions to a large number of systems, including halides, CO, and OCH3− as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds.

Hydrogen bond design principles

Hydrogen bonding principles are at the core of supramolecular design. This overview features a discussion relating molecular structure to hydrogen bond strengths, highlighting the following electronic effects on hydrogen bonding: electronegativity, steric effects, electrostatic effects, π-conjugation, and network cooperativity. Historical developments, along with experimental and computational efforts, leading up to the birth of the hydrogen bond concept, the discovery of nonclassical hydrogen bonds (C-H…O, O-H…π, dihydrogen bonding), and the proposal of hydrogen bond design principles (e.g., secondary electrostatic interactions, resonance-assisted hydrogen bonding, and aromaticity effects) are outlined. Applications of hydrogen bond design principles are presented.

X-ray Photoionization Cross Section Spectra of Water and Ammonia Bonded on Polycyclic Aromatic Hydrocarbons: A Quantum Mechanical Interpretation to the Absorption Spectra on Graphene

A theoretical study of the K-shell total photoabsorption and photoionization cross section spectra of water and ammonia bonded to benzene (C₆H₆) and the polycyclic aromatic hydrocarbons (PAHs) naphthalene (C₁₀H₈), coronene (C₂₄H₁₂) and circumcoronene (C₅₄H₁₈) by van der Waals (vdW) forces is presented. The discretized electronic pseudospectra at the oxygen and nitrogen K-edges, covering the discrete and the continuum spectral regions, were obtained at the time-dependent density functional theory (TDDFT) level with dispersion correction. An analytic continuation procedure based on the Padé approximants was used in order to obtain the K-shell cross sections of the structures at the discrete and the continuum regions of the spectra. By examining the electronic spectra of water and ammonia bonded to coronene and circumcoronene, we observed that our results agree well with the experiments performed with graphene. This work provides a quantum mechanical interpretation to the NEXAFS experiments of water and ammonia adsorbed on graphene in terms of a physisorption model of these molecules by van der Waals forces.

Can the roles of polar and non-polar moieties be reversed in non-polar solvents?

Using thermodynamic integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarities, ranging from the most polar water to the most non-polar cyclohexane.