Incisive probing of intermolecular interactions in molecular crystals: core level spectroscopy combined with density functional theory

Nearly-freestanding supramolecular assembly with tunable structural properties

The synthesis and design of two-dimensional supramolecular assemblies with specific functionalities is one of the principal goals of the emerging field of molecule-based electronics, which is relevant for many technological applications. Although a large number of molecular assemblies have been already investigated, engineering uniform and highly ordered two-dimensional molecular assemblies is still a challenge. Here we report on a novel approach to prepare wide highly crystalline molecular assemblies with tunable structural properties. We make use of the high-reactivity of the carboxylic acid functional moiety and of the predictable structural features of non-polar alkane chains to synthesize 2D supramolecular assemblies of 4-(decyloxy)benzoic acid (4DBA;C[Formula: see text]H[Formula: see text]O[Formula: see text]) on a Au(111) surface. By means of scanning tunneling microscopy, density functional theory calculations and photoemission spectroscopy, we demonstrate that these molecules form a self-limited highly ordered and defect-free two-dimensional single-layer film of micrometer-size, which exhibits a nearly-freestanding character. We prove that by changing the length of the alkoxy chain it is possible to modify in a controlled way the molecular density of the "floating" overlayer without affecting the molecular assembly. This system is especially suitable for engineering molecular assemblies because it represents one of the few 2D molecular arrays with specific functionality where the structural properties can be tuned in a controlled way, while preserving the molecular pattern.

Determination of H-Atom Positions in Organic Crystal Structures by NEXAFS Combined with Density Functional Theory: a Study of Two-Component Systems Containing Isonicotinamide

It is important to be able to identify the precise position of H-atoms in hydrogen bonding interactions to fully understand the effects on the structure and properties of organic crystals. Using a combination of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory (DFT) quantum chemistry calculations, we demonstrate the sensitivity of core-level X-ray spectroscopy to the precise H-atom position within a donor-proton-acceptor system. Exploiting this sensitivity, we then combine the predictive power of DFT with the experimental NEXAFS, confirming the H-atom position identified using single-crystal X-ray diffraction (XRD) techniques more easily than using other H-atom sensitive techniques, such as neutron diffraction. This proof of principle experiment confirms the H-atom positions in structures obtained from XRD, providing evidence for the potential use of NEXAFS as a more accurate and easier method of locating H-atoms within organic crystals.

para-Aminobenzoic acid-capped hematite as an efficient nanocatalyst for solvent-free CO2 fixation under atmospheric pressure

Utilization of carbon dioxide by converting it into value-added chemicals is a sustainable remedy approach that stipulates abundant, cheap, non-toxic and efficient catalytic materials. In this study, we have demonstrated the use of para-aminobenzoic acid-capped hematite (PABA@α-Fe₂O₃) as an efficient nanocatalyst for the conversion of epoxides to cyclic carbonates utilizing CO₂. The developed PABA@α-Fe₂O₃ nanocatalyst along with a cocatalyst, tetrabutylammonium iodide (TBAI), was able to convert a variety of epoxide substrates into their corresponding cyclic carbonates under atmospheric pressure and solvent-free conditions. The efficient catalytic activity of the material is attributed to the synergistic effect between α-Fe₂O₃ and the amine group of the PABA molecule present on the surface. Furthermore, the recyclability study and post-catalytic analysis revealed that the developed catalyst can be used for multiple catalytic cycles due to the stable and robust nature of the nanocatalyst. The choice of the PABA@α-Fe₂O₃ nanocatalyst is indeed a sustainable approach from the CO₂ capture and utilization point of view.

Hybrid silica micro-particles with light-responsive surface properties and Janus-like character

The present work highlights the synthesis and post-modification of silica-based micro-particles containing photo-responsive polymer brushes with photolabile o-nitrobenzyl ester (o-NBE) chromophores.

A nature-inspired hydrogen-bonded supramolecular complex for selective copper ion removal from water

Herein, we present a scalable approach for the synthesis of a hydrogen-bonded organic–inorganic framework via coordination-driven supramolecular chemistry, for efficient remediation of trace heavy metal ions from water. In particular, using copper as our model ion of interest and inspired by nature’s use of histidine residues within the active sites of various copper binding proteins, we design a framework featuring pendant imidazole rings and copper-chelating salicylaldoxime, known as zinc imidazole salicylaldoxime supramolecule. This material is water-stable and exhibits unprecedented adsorption kinetics, up to 50 times faster than state-of-the-art materials for selective copper ion capture from water. Furthermore, selective copper removal is achieved using this material in a pH range that was proven ineffective with previously reported metal–organic frameworks. Molecular dynamics simulations show that this supramolecule can reversibly breathe water through lattice expansion and contraction, and that water is initially transported into the lattice through hopping between hydrogen-bond sites.

Heavy metals and metalloids pose major threats to health and environmental ecosystems, thus systems for low-cost remediation are needed. Here the authors report the scalable design of a hydrogen-bonded organic–inorganic framework for selective removal of trace heavy metal ions from water.

Study of C K-Edge High Energy Resolution Energy-Loss Near-Edge Structures of Copper Phthalocyanine and Its Chlorinated Molecular Crystals by First-Principles Band Structure Calculations

High energy resolution energy-loss near-edge structures (ELNES) at the carbon K-edge of copper phthalocyanine (CuPc) and its chlorinated molecular crystals were observed using electron energy-loss spectroscopy combined with a scanning transmission electron microscope equipped with a monochromator. The ELNES spectra were investigated using first-principles band structure calculations with a core-hole introduced into the 1s orbitals of the nonequivalent C atoms. The calculated spectra including half a core-hole were consistent with the experimental spectra. The spectral features could be interpreted in terms of the different contributions of the partial density of states (PDOS) of nonequivalent C atoms with different transition energies depending on the site. The core-hole effects were also discussed using the spatial distribution of unoccupied states and PDOSs, which revealed site-dependent core-hole effects, where a C atom with a strong spatial distribution intensity of the unoccupied states in the ground state (GS) are susceptible to the core-hole effects. The spectral changes due to chlorination of the CuPc molecule were mainly attributed to an increase of the threshold energy of the C atoms bonded to chlorine, and the influence of the change in the PDOS by chlorination was not significantly large.

Conformational and structural stability of the single molecule and hydrogen bonded clusters of para aminobenzoic acid in the gas and solution phases

The structures of α- and β-para aminobenzoic acid are deconstructed into their hydrogen bonding molecular structural building blocks, where they are analysed usingab initioquantum mechanical calculations of their conformation and cluster stability in solution.

Intermolecular bonding of hemin in solution and in solid state probed by N K-edge X-ray spectroscopies

X-ray absorption/emission spectroscopy (XAS/XES) at the N K-edge of iron protoporphyrin IX chloride (FePPIX-Cl, or hemin) has been carried out for dissolved monomers in DMSO, dimers in water and for the solid state. This sequence of samples permits identification of characteristic spectral features associated with the hemin intermolecular bonding. These characteristic features are further analyzed and understood at the molecular orbital (MO) level based on the DFT calculations.

NEXAFS Sensitivity to Bond Lengths in Complex Molecular Materials: A Study of Crystalline Saccharides

Detailed analysis of the C K near-edge X-ray absorption fine structure (NEXAFS) spectra of a series of saccharides (fructose, xylose, glucose, galactose, maltose monohydrate, α-lactose monohydrate, anhydrous β-lactose, cellulose) indicates that the precise determination of IPs and σ* shape resonance energies is sensitive enough to distinguish different crystalline saccharides through the variations in their average C-OH bond lengths. Experimental data as well as FEFF8 calculations confirm that bond length variations in the organic solid state of 10(-2) Å can be experimentally detected, opening up the possibility to use NEXAFS for obtaining incisive structural information for molecular materials, including noncrystalline systems without long-range order such as dissolved species in solutions, colloids, melts, and similar amorphous phases. The observed bond length sensitivity is as good as that originally reported for gas-phase and adsorbed molecular species. NEXAFS-derived molecular structure data for the condensed phase may therefore be used to guide molecular modeling as well as to validate computationally derived structure models for such systems. Some results indicate further analytical value in that the σ* shape resonance analysis may distinguish hemiketals from hemiacetals (i.e., derived from ketoses and aldoses) as well as α from β forms of otherwise identical saccharides.

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.

Self-association of organic solutes in solution: a NEXAFS study of aqueous imidazole

N K-edge near-edge X-ray absorption fine-structure (NEXAFS) spectra of imidazole in concentrated aqueous solutions have been acquired. The NEXAFS spectra of the solution species differ significantly from those of imidazole monomers in the gas phase and in the solid state of imidazole, demonstrating the strong sensitivity of NEXAFS to the local chemical and structural environment. In a concentration range from 0.5 to 8.2 mol L⁻¹ the NEXAFS spectrum of aqueous imidazole does not change strongly, confirming previous suggestions that imidazole self-associates are already present at concentrations more dilute than the range investigated here. We show that various types of electronic structure calculations (Gaussian, StoBe, CASTEP) provide a consistent and complete interpretation of all features in the gas phase and solid state spectra based on ground state electronic structure. This suggests that such computational modelling of experimental NEXAFS will permit an incisive analysis of the molecular interactions of organic solutes in solutions. It is confirmed that microhydrated clusters with a single imidazole molecule are poor models of imidazole in aqueous solution. Our analysis indicates that models including both a hydrogen-bonded network of hydrate molecules, and imidazole–imidazole interactions, are necessary to explain the electronic structure evident in the NEXAFS spectra.

The solid state, surface and morphological properties of p-aminobenzoic acid in terms of the strength and directionality of its intermolecular synthons

The lattice energy and crystal morphologies of the α and β forms of p-aminobenzoic acid are correlated to experimentally grown crystals by calculating their strength, directionality and chemical state of their bulk (intrinsic) and surface (extrinsic) synthons.