Benzene Forms Hydrogen Bonds with Water

A close competition between O–H⋯O and O–H⋯π hydrogen bonding: IR spectroscopy of anisole–methanol complex in helium nanodroplets

Anisole forms O–H⋯O as well O–H⋯π bound complexes with methanol.

Progressive Hydrophobicity of Fluorobenzenes

The potentials of mean force for the dimers of fluorobenzenes sample both π-stacked and T-shaped structures for partially fluorinated benzenes, namely, 1,4-difluorobenzene, 1,3,5-trifluorobenzene, and 1,2,4,5-tetrafluorobenzene, and sample only the T-shaped structures for benzene and hexafluorobenzene. While the free energy for the dimerization in water is very weakly dependent on the number of fluorine atoms, the formation of π-stacked structures is entropy-driven and the T-shaped structures appear due to an enthalpic minimum. Interestingly, the solvation behavior suggests that the accumulation of water around the contact and solvent-separated pairs decreases with the increase in the number of fluorine atoms, which signifies progressive hydrophobicity of fluorobenzenes.

Enthalpy-Entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water

Aromatic groups can engage in an interesting class of noncovalent interactions termed π-π interactions, which play a pivotal role in stabilizing a variety of molecular architectures, including nucleic acids, proteins, and supramolecular assemblies. When the aromatic compounds interact with each other in an aqueous environment, their association is facilitated by the hydrophobic effect-the trend of nonpolar solutes to aggregate in a polar solution. To develop an in-depth understanding of hydrophobic association, we investigate in the present work π-π interactions in water, employing as a paradigm the benzene dimer. Using DFT-CES, a mean-field QM/MM method recently developed by our group, we describe the benzene solute at a quantum-mechanical level. Full consideration of detailed solute-electron density enables an optimal description of the solute-solvent interactions, leading to an accurate prediction of hydration free energies. In π-stacking of benzene, we find an entropic stabilization associated with the shrinkage of the solvent-excluded volume, which agrees with the theory of hydrophobic effect at subnanoscales. However, at the equilibrium binding distance of the benzene dimer, we find that the entropic stabilization nearly cancels out due to the enthalpic cost required for dewetting the internal space. Such an enthalpy-entropy compensation leads the association free energy to be predominantly dictated by the solute-solute interaction enthalpy. The present work offers new insight into the mechanistic role of water and the primary thermodynamic driving force of hydrophobic association.

Raising glass transition temperature of polymer nanofilms as a function of negative interface energy

Based on a thermodynamic approach, glass transition temperature (T_g) of substrate-supported polymer nanofilms (s-PNFs) is investigated for carbon-chain polymers, taking the role of the interface energy into consideration.

Force Fields for Small Molecules

Molecular dynamics (MD) simulations have been widely applied to computer-aided drug design (CADD). While MD has been used in a variety of applications such as free energy perturbation and long-time simulations, the accuracy of the results from those methods depends strongly on the force field used. Force fields for small molecules are crucial, as they not only serve as building blocks for developing force fields for larger biomolecules but also act as model compounds that will be transferred to ligands used in CADD. Currently, a wide range of small molecule force fields based on additive or nonpolarizable models have been developed. While these nonpolarizable force fields can produce reasonable estimations of physical properties and have shown success in a variety of systems, there is still room for improvements due to inherent limitations in these models including the lack of an electronic polarization response. For this reason, incorporating polarization effects into the energy function underlying a force field is believed to be an important step forward, giving rise to the development of polarizable force fields. Recent simulations of biological systems have indicated that polarizable force fields are able to provide a better physical representation of intermolecular interactions and, in many cases, better agreement with experimental properties than nonpolarizable, additive force fields. Therefore, this chapter focuses on the development of small molecule force fields with emphasis on polarizable models. It begins with a brief introduction on the importance of small molecule force fields and their evolution from additive to polarizable force fields. Emphasis is placed on the additive CHARMM General Force Field and the polarizable force field based on the classical Drude oscillator. The theory for the Drude polarizable force field and results for small molecules are presented showing their improvements over the additive model. The potential importance of polarization for their application in a wide range of biological systems including CADD is then discussed.

Interactions between azines and alcohols: a rotational study of pyridine–tert-butyl alcohol

The observed spectrum identifies aC_ssymmetry σ-type complex, with the two subunits held together by coplanar “classical” O–H⋯N and weak C–H⋯π intermolecular hydrogen bonds. The O⋯N distance decreases by 4 mÅ upon deuteration of the hydroxyl group (reverse Ubbelohde effect).

Microwave spectrum and non-covalent interactions of the 1, 2, 3, 4-tetrafluorobenzene-water complex

The 1, 2, 3, 4-tetrafluorobenzene-water complex was investigated by pulsed-jet Fourier transform microwave spectroscopy. One isomer was detected in the jet expansion. Ab initio calculations and non-covalent interaction (NCI) analysis were performed to characterize the intermolecular NCIs. In the observed isomer, the water molecule lies almost in the plane of the benzene ring acting as a proton donor to one of the fluorine atoms and as an acceptor to one of the hydrogen atoms forming a six-membered ring structure. The CH⋯O and H⋯FC bonding distances are determined to be 2.385(1) Å and 2.429(1) Å, respectively. The interaction energy is calculated to be -18.0 kJ mol^-1 at the SAPT2+(3)/aug-cc-pVDZ level of theory. The observed transitions exhibit splitting in the order of tens to hundreds of kHz due to the internal rotation of water moiety. The possible tunneling paths of water were investigated by ab initio calculations resulting in a barrier for an internal rotation of about 201 cm^-1.

Noncovalent Interactions between Molecular Hydrogen and the Alkali Fluorides: H-H···F-M (M = Li, Na, K, Rb, Cs). High Level Theoretical Predictions and SAPT Analysis

Various types of hydrogen bonds have been recognized during the past century. In this research, a new type of noncovalent interaction, the dipole-induced hydrogen bond formed between a hydrogen molecule and an alkali halide, H-H···F-M, is studied. Proposed by Zhang and co-workers ( Phys. Chem. Chem. Phys. 2015, 17, 20361), these systems are extensively investigated initially using the "gold standard" CCSD(T) method in conjunction with augmented correlation-consistent polarized core-valence basis sets up to quadruple-ζ. The full triple excitations CCSDT method has been used to further refine the energies. Several properties including geometries, bond energies, vibrarional frequencies, charge distributions, and dipole moments have been reported. The earlier Zhang research considered only the linear H-H···F-M structures. However, we find these linear stationary points to be separated by very small barriers from the much lower lying bent C _s structures. The CCSDT/aug-cc-pCVQZ(-PP) method predicts the dissociation energies for bent H-H···F-M (M = Li, Na, K, Rb, Cs) are 2.76, 2.96, 3.00, 2.89, and 2.49 kcal mol^-1, respectively, suggesting that the H···F hydrogen bond becomes gradually stronger when alkali metal M goes down the periodic table from Li to K but becomes slightly weaker for Rb and even more for Cs. This Li < Na < K > Rb > Cs order is consistent with that for the dipole moments for the isolated MF (M = Li, Na, K, Rb, Cs) diatomics. Symmetry adapted perturbation theory (SAPT) is used to understand these unusual noncovalent interactions.

Similarities and differences in the crystal packing of halogen-substituted indole derivatives

The role of different intermolecular interactions in the crystal structures of halogen-substituted indoles which are fused with six-membered or seven-membered cyclic rings is investigated here. Several crystal structures show isostructural characteristics due to the presence of similar supramolecular motifs. In the absence of any strong hydrogen bonds, the molecular packing of reported structures is primarily stabilized by the presence of non-classical N-H...π and C-H...π interactions in addition to C-H...X (X = F/Cl/Br) interactions. The nature and energetics of primary and secondary dimeric motifs are partitioned into the electrostatics, polarization, dispersion and exchange-repulsion components using the PIXEL method. Short and directional N-H...π interactions are further explored by a topological analysis of the electron density based on quantum theory of atoms in molecules.

Dynamics of water in conical solvation shells around a benzene solute under different thermodynamic conditions

Water molecules in different parts of the anisotropic hydration shell of an aromatic molecule experience different interactions. In the present study, we investigate the anisotropic dynamics of water molecules in different non-overlapping conical shells around a benzene solute at sub- and supercritical conditions by means of molecular dynamics simulations using both non-polarizable and polarizable models. In addition to the dynamical properties, the effects of polarizability on the hydration structure of benzene at varying thermodynamic conditions are also investigated in the current study. The presence of πH-bonding in the solvation shell is found to be an important factor that influences the anisotropic dynamics of the benzene hydration shell. The water molecules located axial to the benzene plane are found to be maximally influenced by the πH-bonding. The extent of πH-bonding is found to be somewhat reduced on inclusion of polarizability. The πH-bonded water molecules are found to reorient through large-amplitude angular jumps where the jump-angle amplitude increases at higher temperatures and lower densities. For both non-polarizable and polarizable models, it is found that the water molecules in the axial conical shells possess faster orientational and hydrogen bond dynamics compared to those in the equatorial plane. Water molecules in the axial conical shells are also found to diffuse at a faster rate than bulk molecules due to the relatively weaker benzene-water πH-bonding interactions in the axial region of the hydration shell. The residence dynamics of water molecules in different conical solvation shells around the solute is also investigated in the current study.

Improving the first hyperpolarizability of anthracene through interaction with HX molecules (XF, Cl, Br): A theoretical study

The variations in nonlinear optical activity (NLO) of anthracene (C₁₄H₁₀) was investigated via intermolecular interactions between C₁₄H₁₀ and HX molecules (XF, Cl and Br) using B3LYP-D3 method at 6-311++G(d,p) basis set. The stabilization of those complexes was investigated via vibrational analysis, quantum theory of atoms in molecules, molecular electrostatic potential, natural bond orbitals and symmetry-adapted perturbation theory (SAPT) analysis. Furthermore, the optical spectra and the first hyperpolarizabilities of C₁₄H₁₀⋯HX complexes were computed. The adsorption of hydrogen halide through C₁₄H₁₀⋯HX complex formation, didn't change much the linear optical activities of C₁₄H₁₀ molecule, but the magnitude of the first hyperpolarizability of the C₁₄H₁₀⋯HX complexes to be as much as that of urea.

Microhydration of PAH+ cations: evolution of hydration network in naphthalene+-(H2O) n clusters (n ≤ 5)

The interaction of polycyclic aromatic hydrocarbon molecules with water (H2O = W) is of fundamental importance in chemistry and biology. Herein, size-selected microhydrated naphthalene cation nanoclusters, Np+-W n (n ≤ 5), are characterized by infrared photodissociation (IRPD) spectroscopy in the C-H and O-H stretch range to follow the stepwise evolution of the hydration network around this prototypical PAH+ cation. The IRPD spectra are highly sensitive to the hydration structure and are analyzed by dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ) to determine the predominant structural isomers. For n = 1, W forms a bifurcated CH···O ionic hydrogen bond (H-bond) to two acidic CH protons of the bicyclic ring. For n ≥ 2, the formation of H-bonded solvent networks dominates over interior ion solvation, because of strong cooperativity in the former case. For n ≥ 3, cyclic W n solvent structures are attached to the CH protons of Np+. However, while for n = 3 the W3 ring binds in the CH···O plane to Np+, for n ≥ 4 the cyclic W n clusters are additionally stabilized by stacking interactions, leading to sandwich-type configurations. No intracluster proton transfer from Np+ to the W n solvent is observed in the studied size range (n ≤ 5), because of the high proton affinity of the naphthyl radical compared to W n . This is different from microhydrated benzene+ clusters, (Bz-W n )+, for which proton transfer is energetically favorable for n ≥ 4 due to the much lower proton affinity of the phenyl radical. Hence, because of the presence of polycyclic rings, the interaction of PAH+ cations with W is qualitatively different from that of monocyclic Bz+ with respect to interaction strength, structure of the hydration shell, and chemical reactivity. These differences are rationalized and quantified by quantum chemical analysis using the natural bond orbital (NBO) and noncovalent interaction (NCI) approaches.

Hydrogen bond docking preference in furans: OH⋯π vs. OH⋯O

The docking sites of hydrogen bonds in complexes formed between 2,2,2-trifluoroethanol (TFE), furan (Fu), and 2-methyl furan (MF) have been investigated. Using density functional theory (DFT) calculations, gas phase and matrix isolation FTIR spectroscopies, the strengths of OH⋯O and OH⋯π hydrogen bonds in the complexes were compared to find the docking preference. Calculations suggest that the hydrogen bond donor, TFE, is more likely to dock onto the oxygen atom of the aromatic furans ring, and consequently, the OH⋯O type hydrogen bond is relatively stronger than the OH⋯π type. The FTIR spectrum in the OH-stretching fundamental range obtained at room temperatures has been compared with that obtained at extremely low temperatures in the matrix. The fundamental and the red shifts of OH-stretching vibrations were observed in both FTIR spectra, confirming the formation of hydrogen bonded complexes. By assessing the ability of furan and MF to participate in the formation of OH⋯O hydrogen bond, the effect of ring methylation has been highlighted. From the calculated geometric and thermodynamic parameters as well as the frequency shift of the OH-stretching vibrations in complexes, TFE-MF is found to be more stable than TFE-Fu, which suggests that the strength of the OH⋯O hydrogen bond in TFE-MF originates from the high activity of the furan molecule caused by the methylation of the aromatic ring. The present study furthers the knowledge of docking preference in heteroaromatic molecules and is helpful to understand the nature of intermolecular interactions between hydrogen bond donors and acceptors, including both electron-deficient atoms and π cloud.

Microwave spectroscopy of 2-(trifluoromethyl)pyridine⋯water complex: Molecular structure and hydrogen bond

In order to explore the -CF₃ substitution effect on the complexation of pyridine, we investigated the 2-(trifluoromethyl)pyridine⋯water complex by using pulsed jet Fourier transform microwave spectroscopy complemented with quantum chemical calculations. Experimental assignment and ab initio calculations confirmed that the observed complex is stabilized through N⋯H-O and O⋯H-C hydrogen bonds forming a five-membered ring structure. The bonding distance in N⋯H-O is determined to be 2.027(2) Å, whilst that in O⋯H-C interaction is 2.728(2) Å. The quantum theory of atoms in molecules analysis indicates that the interaction energy of N⋯H-O hydrogen bond is ∼22 kJ mol^-1 and that for O⋯H-C hydrogen bond is ∼5 kJ mol^-1. The water molecule lies almost in the plane of the aromatic ring in the complex. The -CF₃ substitution to pyridine quenches the tunneling splitting path of the internal motion of water molecule.

Capturing the Elusive Water Trimer from the Stepwise Growth of Water on the Surface of the Polycyclic Aromatic Hydrocarbon Acenaphthene

Polycyclic aromatic hydrocarbons (PAHs) are key players in reaction chemistry. While it is postulated that they serve as a basis for ice grains, there has been no direct detection of PAHs in astronomical environments. We aim to investigate the hydration of PAHs to set a foundation for the future exploration of potential ice formation pathways. We report results from chirped pulse Fourier transform microwave spectroscopy and quantum-chemical calculations for the PAH acenaphthene and acenaphthene complexed with up to four water molecules. The acenaphthene-(H₂O)₃ complex is of particular interest as the elusive cyclic water trimer was observed. It appears in a slightly distorted configuration when compared with the pure water trimer. This is explained by hydrogen-bond net cooperativity effects. Binding energies for the complexes are presented. Our results provide insight into the onset of complex aggregation that could be occurring in extraterrestrial environments as part of ice grain formation.

Weak Hydrogen Bond Network: A Rotational Study of 1,1,1,2-Tetrafluoroethane Dimer

1,1,1,2-Tetrafluoroethane dimer was investigated by pulsed jet Fourier transform microwave spectroscopy. One conformer, stabilized through a network of four C-H···F-C interactions, was observed, although several almost isoenergetic configurations were suggested by ab initio calculations. The measurements, extended to four ¹³C species in natural abundance, allowed determination of the carbon skeleton structures and evaluation of the weak hydrogen bond parameters. Information on the dissociation energy is also provided.

Photolysis of polycyclic aromatic hydrocarbons (PAHs) on Fe3+-montmorillonite surface under visible light: Degradation kinetics, mechanism, and toxicity assessments

Photochemical behavior of various polycyclic aromatic hydrocarbons (PAHs) on Fe³⁺-modified montmorillonite was explored to determine their potential kinetics, pathways, and mechanism under visible light. Depending on the type of PAH molecules, the transformation rate follows the order of benzo[a]pyrene ≈ anthracene > benzo[a]anthracene > phenanthrene. Quantum simulation results confirm the crucial role of "cation-π" interaction between Fe³⁺ and PAHs on their transformation kinetics. Primary intermediates, including quinones, ring-opening products and benzene derivatives, were identified by gas chromatography-mass spectrometer (GC-MS), and the possible photodegradation pathway of benzo[a]pyrene was proposed. Meanwhile, radical intermediates, such as reactive oxygen species (ROS) and free organic radicals, were detected by electron paramagnetic resonance (EPR) technique. The photolysis of selected PAHs, such as anthracene and benzo[a]pyrene, on clay surface firstly occurs by electron transfer from PAHs to Fe³⁺-montmorillonite, followed by degradation involving photo-induced ROS such as ·OH and ·O₂^-. To investigate the acute toxicity of photolysis products, the Microtox^® toxicity test was performed during the photodegradation processes of various PAHs. As a result, the photo-irradiation initially induces increased toxicity by generating reactive intermediates, such as free organic radicals, and then the toxicity gradually decreases with increasing of reaction time. Overall, the present study provides useful information to understand the fate and photo-transformation of PAHs in contaminated soils.

Retention of poly(N-isopropylacrylamide) on 3-aminopropyltriethoxysilane

Silane coupling agents are commonly employed to link an organic polymer to an inorganic substrate. One of the widely utilized coupling agents is 3-aminopropyltriethoxy silane (APTES). In this study, the authors investigated the ability of APTES to retain thermo-responsive poly(N-isopropylacrylamide) (pNIPAAm) on hydroxylated surfaces such as glass. For comparison purposes, the authors also evaluated the retention behaviors of (1) polystyrene, which likely has weaker van der Waals interactions and acid-base interactions (contributed by hydrogen-bonding) with APTES, on APTES as well as (2) pNIPAAm on two other silane coupling agents, which have similar structures to APTES, but exhibit less interaction with pNIPAAm. Under our processing conditions, the stronger interactions, particularly hydrogen bonding, between pNIPAAm and APTES were found to contribute substantially to the retention of pNIPAAm on the APTES modified surface, especially on the cured APTES layer when the interpenetration was minimal or nonexistent. On the noncured APTES layer, the formation of an APTES-pNIPAAm interpenetrating network resulted in the retention of thicker pNIPAAm films. As demonstrated by water contact angles [i.e., 7°-15° higher at 40 °C, the temperature above the lower critical solution temperature (LCST) of 32 °C for pNIPAAm, as compared to those at 25 °C] and cell attachment and detachment behaviors (i.e., attached/spread at 37 °C, above LCST; detached at 20 °C, below LCST), the retained pNIPAAm layer (6-15 nm), on both noncured and cured APTES, exhibited thermo-responsive behavior. The results in this study illustrate the simplicity of using the coupling/adhesion promoting ability of APTES to retain pNIPAAm films on hydroxylated substrates, which exhibit faster cell sheet detachment (≤30 min) as compared to pNIPAAm brushes (in hours) prepared using tedious and costly grafting approaches. The use of adhesion promoters to retain pNIPAAm provides an affordable alternative to current thermo-responsive supports for cell sheet engineering and stem cell therapy applications.

Unraveling the Molecular Weight Dependence of Interfacial Interactions in Poly(2-vinylpyridine)/Silica Nanocomposites

The structure and polymer-nanoparticle interactions among physically adsorbed poly(2-vinylpyridine) chains on the surface of silica nanoparticles (NPs) were systematically studied as a function of molecular weight (MW) by sum frequency generation (SFG) and X-ray photoelectron (XPS) spectroscopies. Analysis of XPS data identified hydrogen bonds between the polymer and NPs, while SFG evaluated the change in the number of free OH sites on the NP's surface. Our data revealed that the hydrogen bonds and amount of the free -OH sites have a significant dependence on the polymer's MW. These results provide clear experimental evidence that the interaction of physically adsorbed chains with nanoparticles is strongly MW dependent and aids in unraveling the microscopic mechanism responsible for the strong MW dependence of dynamics of the interfacial layer in polymer nanocomposites.

Beyond the electrostatic model: the significant roles of orbital interaction and the dispersion effect in aqueous–π systems

The importance of orbital interaction in aqueous–π interactions is explored in detail and a unified description is proposed.

Privileged hydration sites in aromatic side chains: effect on conformational equilibrium

The most energetically favourable hydration sites of aromatic (Phe, Tyr, Trp and His) side chains revealed by DFT-based theoretical calculations.

Corannulene and its complex with water: a tiny cup of water

We report the results of a broadband rotational spectroscopic study of corannulene, C₂₀H₁₀, all of its singly substituted ¹³C isotopologues, and a complex of corannulene with one molecule of water.

On the structure of prilocaine in aqueous and amphiphilic solutions

The solvation of prilocaine has been investigated in pure water and in amphiphilic solutions using a combination of neutron diffraction and simulations.

Behavior of interactions between hydrogen chalcogenides and an anthracene π-system elucidated by QTAIM dual functional analysis with QC calculations

The nature of the interactions between chalcogenides and the anthracene p-system, EH₂-*-p(C₁₄H₁₀), is predicted to be close to that of EH₂-*-p(C₁₀H₈), although the partial structures around the central rings can be found in EH₂-*-p(C₆H₆).

Infrared spectroscopy of hydrated polycyclic aromatic hydrocarbon cations: naphthalene+–water

The combination of infrared spectroscopy and quantum chemical calculations unravels the salient properties of the bifurcated CH⋯O ionic hydrogen bond typical for the PAH⁺–H₂O interaction.