Selective effect of guest molecule length and hydrogen bonding on the supramolecular host structure

A host supramolecular structure consisting of bis-(2,2':6',2' '-terpyridine)-4'-oxyhexadecane (BT-O-C16) is shown to respond to guest molecules in dramatic ways, as observed by using scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite surface under ambient conditions. It is observed that small linear molecules can be encapsulated within the host supramolecular lattice. The characteristics of the host structure were nearly unaffected by the encapsulated guest molecules of terphthalic acid (TPA) dimers, whereas appreciable changes in cavity dimension can be observed with azobenzene-4,4'-dicarboxylic acid. The STM study and density functional theory (DFT) analysis reveal that intermolecular hydrogen bonding interaction plays an essential role in forming the assembling structures. The difference in guest molecule length is considered the important cause for the different guest-host complexes.     

Valence electronic properties of n-channel organic materials based on fluorinated derivatives of perylene diimides

The valence electronic states of three kinds of fluorinated derivatives of perylene diimides, D2MFPP, D3MFPP, and D4MFPP, on Cu(110) and SiO(2)Si surface were studied by photoemission and density functional calculations. When these organic molecules were deposited on the Cu(110) and thermally oxidized SiO(2) surfaces, five well-resolved photoemission features originating from the molecules were observed. On Cu(110) surface, two emission features with pi-like character increased their binding energy with increasing the coverage of organic molecule, indicating a strong interaction between the organic molecules and Cu substrate. The density functional calculations suggest flat-lying adsorption geometry for D3MFPP and D4MFPP on Cu(110) surface.     

Effects of Organic Compounds on the Electrocrystallization of Nickel

It is shown how electrodeposited nickel crystallizes from a Watts bath containing different organic compounds. Rigaku-Denki Geigerfiex DS X-ray diffractometer is used to determine the preferred orientation. Factors determining the development of the coating texture are discussed and the adsorption at a metallic solid surface is considered. The possibilities of the appearance of the oriented adsorption in the process are also discussed. The oriented adsorption of the studied organic compounds on crystallographic planes of nickel is presented in the discussion. There is a direct relationship between the degree of random orientation and brightness. Random orientation is attributed to domination of growth inhibition of the normally faster growing lattice plane. Growth inhibition of lattice planes depends on the oriented adsorption of molecules of the organic compounds.     

D-penicillamine adsorption on gold: an in situ ATR-IR spectroscopic and QCM study

The adsorption of penicillamine from ethanol on gold was studied in situ by attenuated total reflection infrared (ATR-IR) and quartz crystal microbalance (QCM) experiments. Both ATR-IR and QCM reveal a fast mass uptake. In ethanol, the molecule adopts a zwitterionic form. Upon adsorption, part of the molecules deprotonate at the amine group, which is a relatively slow process that goes along with a strong shift of the nu(as)(COO(-)) mode. Both ATR-IR and QCM confirm a physisorbed layer. ATR-IR furthermore shows that the latter consists of zwitterionic molecules only, whereas both zwitterionic and anionic species are found in the chemisorbed layer. The infrared spectra of the physisorbed and chemisorbed layers are rather different, and the molecules within both layers seem to be oriented with respect to the surface. The ATR-IR spectra furthermore indicate that all three functional groups of penicillamine (i.e., thiol, carboxylate, and amine) interact with the surface, and density functional theory calculations support this finding. QCM also shows that the molecule uses considerably more space on the surface than molecules of similar size, which supports a three-point interaction. The latter leads to a strong anchoring of the molecule to the metal, which may explain the exceptional capability of penicillamine to bind metals.     

Surface supramolecular organization of a terbium(III) double-decker complex on graphite and its single molecule magnet behavior

The two-dimensional self-assembly of a terbium(III) double-decker phthalocyanine on highly oriented pyrolitic graphite (HOPG) was studied by atomic force microscopy (AFM), and it was shown that it forms highly regular rectangular two-dimensional nanocrystals on the surface, that are aligned with the graphite symmetry axes, in which the molecules are organized in a rectangular lattice as shown by scanning tunneling microscopy. Molecular dynamics simulations were run in order to model the behavior of a collection of the double-decker complexes on HOPG. The results were in excellent agreement with the experiment, showing that-after diffusion on the graphite surface-the molecules self-assemble into nanoscopic islands which align preferentially along the three main graphite axes. These low dimension assemblies of independent magnetic centers are only one molecule thick (as shown by AFM) and are therefore very interesting nanoscopic magnetic objects, in which all of the molecules are in interaction with the graphite substrate and might therefore be affected by it. The magnetic properties of these self-assembled bar-shaped islands on HOPG were studied by X-ray magnetic circular dichroism, confirming that the compounds maintain their properties as single-molecule magnets when they are in close interaction with the graphite surface.     

Functional Group Modification and Bonding Characteristics of Ti3C2 MXene-Organic Composites from First-Principles Calculations

The unique physical structure and abundant surface functional groups of MXene make the grafted organic molecules exhibit specific electrical and optical properties. This work reports the results of first-principles calculations to investigate the composite systems formed by different organic molecular monomers, namely acrylic acid (AA), acrylamide (AM), 1-aziridineethanol (1-AD) and glucose, and Ti₃C₂ MXene saturated with different functional groups, namely −OH, −O and −F. The results show that the interaction between organic molecules and the MXene surface depends on the type of functional groups of the organic molecules, while the strength of the interaction is determined by the type of surface functional groups and the number of hydrogen bonds. The bare Ti₃C₂ and Ti₃C₂(OH)₂ can readily form strong chemical and hydrogen bonds with AA and AM molecules, leading to strong adsorption energy and a large amount of charge transfer, while the interaction between organic molecules and MXene saturated by −F or −O groups mainly exhibits physical interactions, accompanied by low adsorption energy and a small amount of charge transfer. This research provides theoretical guidance for the synthesis of high-performance MXene organic composite systems.     

A Theoretical Study of the Interaction of Hydrogen and Oxygen with Palladium or Gold Adsorbed on Pyridine‐Like Nitrogen‐Doped Graphene

The interaction of H₂ and O₂ molecules in the presence of nitrogen‐doped graphene decorated with either a palladium or gold atom was investigated by using density functional theory. It was found that two hydrogen molecules were adsorbed on the palladium atom. The interaction of these adsorbed hydrogen molecules with two oxygen molecules generates two hydrogen peroxide molecules first through a Eley–Rideal mechanism and then through a Langmuir–Hinshelwood mechanism. The barrier energies for this reaction were small; therefore, we expect that this process may occur spontaneously at room temperature. In the case of gold, a single hydrogen molecule is adsorbed and dissociated on the metal atom. The interaction of the dissociated hydrogen molecule on the surface with one oxygen molecule generates a water molecule. The competitive adsorption between oxygen and hydrogen molecules slightly favors oxygen adsorption.     

Intermolecular H···O═C bonds induced 2D self‐assembly of thiophene based diketopyrrolopyrrole derivative

Compounds with diketopyrrolopyrrole (DPP) and thiophene moieties have attracted considerable attention because of their promising charge transport properties. The molecular conformation and self‐assembly of 2,5‐dihexadecyl‐3,6‐di(thiophen‐2‐yl)‐2,5‐dihydropyrrolo[3,4‐c]pyrrole‐1,4‐dione (TDPP‐C16) molecule have been investigated by scanning tunneling microscopy and density functional theory alculation. The TDPP‐C16 molecules adsorb with their optimized S‐shaped conformation and form a zipper‐like pattern on highly oriented pyrolytic graphite surface. R and S rotated structures are observed. The nanostructure is dominated by intermolecular double hydrogen bonds between C═O of the DPP units and hydrogen atom of thiophene rings in the neighboring molecules in each row. Atomic force microscopy and density functional theory calculation also display the existence of strong intermolecular hydrogen bonding. The results provide molecular evidence for the intermolecular interactions of the surface structure, which could benefit to the design of the organic semiconducting materials and understanding of underlying principle of charge transfer process. Copyright © 2017 John Wiley & Sons, Ltd.     

Nonideal mixing of 16-(9-anthroyloxy) palmitic acid and fatty acid in monolayer

The surface pressure-molecular area curve of the mixed monolayer of 16-(9-anthroyloxy) palmitic acid (16AP) and fatty acid (palmitic or stearic acids) showed various kink points which indicated the phase transitions of the monolayer. On the basis of the surface phase rule, the phase diagrams of the mixed monolayer were elucidated. The bifunctional molecule, 16AP, takes two orientations in a monolayer state, that is, horizontal and vertical ones. Horizontally oriented 16AP and vertically oriented fatty acid form a mixed monolayer but this exhibits deviation from the ideal mixing, which was interpreted in terms of the surface regular solution theory. On the other hand, the 16AP molecule in the vertical state was found to be immiscible with the fatty acid molecule in a monolayer de spite both molecules being vertical to the surface and parallel to each other. This was caused by the participation of the 9-anthroyloxy moiety of 16AP in the interaction of 16AP and fatty acid in the hydrophobic region of the monolayer.     

Scanning tunneling microscopy study of metal-free phthalocyanine monolayer structures on graphite

Low temperature scanning tunneling microscopy (STM) studies of metal-free phthalocyanine (H2Pc) adsorbed on highly oriented pyrolytic graphite (HOPG) have shown ordered arrangement of molecules for low coverages up to 1 ML. Evaporation of H2Pc onto HOPG and annealing of the sample to 670 K result in a densely packed structure of the molecules. Arrangements of submonolayer, monolayer, and monolayer with additional adsorbed molecules have been investigated. The high resolution of our investigations has permitted us to image single molecule orientation. The molecular plane is found to be oriented parallel to the substrate surface and a square adsorption unit cell of the molecules is reported. In addition, depending on the bias voltage, different electronic states of the molecules have been probed. The characterized molecular states are in excellent agreement with density functional theory ground state simulations of a single molecule. Additional molecules adsorbed on the monolayer structures have been observed, and it is found that the second layer molecules adsorb flat and on top of the molecules in the first layer. All STM measurements presented here have been performed at a sample temperature of 70 K.     

Coadsorption-induced reconstruction of supramolecular assembly characteristics.

A host supramolecular structure consisting of bis-(2,2':6',2"-terpyridine)-4'-oxyhexadecane (BT-O-C16) is shown to respond to coadsorbed molecules in dramatic ways, as observed by scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite (HOPG) surface under ambient conditions. Interestingly, the lattice parameter of the triphenylene-filled complex differs significantly from that of the coronene-filled one, although the triphenylene and coronene molecules are nearly the same size. The STM study and density functional theory calculations reveal that intermolecular hydrogen-bond interactions play an essential role in forming the assembly structures. The different electronic properties of coronene and triphenylene molecules are responsible for the difference in lattice parameters and consequently for the difference in filling behaviors in the coronene/BT-O-C16 and triphenylene/BT-O-C16 binary systems.     

Adsorption geometry of 4-picoline chemisorbed on the Cu(110) surface: a study of forces controlling molecular self-assembly

The adsorption of 4-picoline (4-methylpyridine) on the Cu(110) surface has been studied with time-of-flight electron stimulated desorption ion angular distribution (TOF-ESDIAD) and other methods. Using deuterium labeling in the methyl group and hydrogen labeling on the aromatic ring, it has been possible to separately monitor by TOF-ESDIAD the C-D bond directions and the C-H bond directions in the adsorbed molecule. These triangulation measurements have led to a detailed understanding of the conformation of the adsorbed molecule relative to the Cu(110) crystal lattice, allowing one to witness changes in the molecular conformation as adsorbate-adsorbate interactional effects take place for increasing coverages. At low coverages, the molecule adsorbs by the N atom at an atop Cu site with the aromatic ring parallel to the <001> azimuth and with the molecular axis inclined 33 (+/- 5) degrees along the <001> azimuth. As rows of 4-picoline molecules form long range ordered chain structures oriented along the <112> azimuth, the aromatic ring twists 29 degrees about the inclined molecular axis as a result of forces between the adsorbate molecules. The initial tilting of the molecular axis at low coverage is likely due to the interaction of the positive-outward dipole with its image in the substrate. The ring twist may result from dipoleminus signdipole forces between the adsorbate molecules in the rows formed tending to form nested parallel pyridine rings. These studies are the first to apply the TOF-ESDIAD method for the measurement of the direction of chemical bonds at more than one molecular location within an adsorbed molecule and the new method is named electron stimulated desorption-molecular triangulation (ESD-MT). The results obtained give information of importance in understanding the factors which control conformational effects during the molecular self-assembly of complex adsorbed molecules on surfaces.     

外缘烷基链长对共轭有机小分子聚集行为及光电性质影响

改变分子化学结构和调控分子结构聚集态行为从而影响或改变材料的化学和物理性质, 是开发新型高效有机光电功能材料的重要手段. 在共轭有机分子外缘引入烷基链一般是为了改进材料溶解性能, 但近来的一些研究表明, 烷基链长对一些共轭有机小分子固态聚集行为和光电性质具有重要影响, 烷基链扮演着显著调控材料光电性质的“功能基团”作用. 本文以聚集诱导发光（aggregation-induced emission, AIE）/聚集强化荧光（aggregation enhanced emission, AEE）发射共轭有机小分子为重点, 对近年来有关烷基链长对共轭有机分子聚集形态和光电性质影响的一些典型事例进行评述, 旨在使人们在进行共轭有机分子设计合成及其结构与性能关系研究中能够关注烷基链的因素, 使烷基链变化作为功能导向晶态共轭有机材料设计合成及其可控制备的一种手段.     

A computer modeling study of the competitive adsorption of water and organic surfactants at surfaces of the mineral scheelite

Atomistic computer simulation techniques were employed to investigate the interaction of a selection of organic surfactant molecules with a range of scheelite surfaces. The adsorbates coordinate mainly to the surfaces through interaction between their oxygen (or nitrogen) atoms to surface calcium ions, followed by hydrogen-bonded interactions to surface oxygen ions. Bridging between two surface calcium ions is the preferred mode of adsorption, but a bidentate interaction by two adsorbate oxygen ions to the same surface calcium ion is also a stable configuration and multiple interactions between surfaces and adsorbate molecules lead to the largest adsorption energies. All adsorbates containing carbonyl and hydroxy groups interact strongly with the surfaces, releasing energies between approximately 80 and 170 kJ mol(-1), but methylamine containing only the -NH2 functional group adsorbs to the surfaces to a much lesser extent (55-86 kJ mol(-1)). Both hydroxymethanamide and hydroxyethanal adsorb to some surfaces in an eclipsed conformation, which is a requisite for these functional groups. Sorption of the organic material by replacement of preadsorbed water at different surface features is calculated to be mainly exothermic for methanoic acid, but less so for the hydroxymethanamide and hydroxyethanal molecules, whereas methylamine would not replace preadsorbed water at the scheelite surfaces. The efficacy of the surfactant molecules is hence calculated to be carboxylic acids > alkyl hydroxamates > hydroxyaldehydes > alkylamines. The results from this study suggest that computer simulations may provide a route to the identification or even design of particular organic surfactants for use in mineral separation processes.     

Water monomer interaction with gold nanoclusters from van der Waals density functional theory

We investigate the interaction between water molecules and gold nanoclusters Au(n) through a systematic density functional theory study within both the generalized gradient approximation and the nonlocal van der Waals (vdW) density functional theory. Both planar (n = 6-12) and three-dimensional (3D) clusters (n = 17-20) are studied. We find that applying vdW density functional theory leads to an increase in the Au-Au bond length and a decrease in the cohesive energy for all clusters studied. We classify water adsorption on nanoclusters according to the corner, edge, and surface adsorption geometries. In both corner and edge adsorptions, water molecule approaches the cluster through the O atom. For planar clusters, surface adsorption occurs in a O-up/H-down geometry with water plane oriented nearly perpendicular to the cluster. For 3D clusters, water instead favors a near-flat surface adsorption geometry with the water O atom sitting nearly atop a surface Au atom, in agreement with previous study on bulk surfaces. Including vdW interaction increases the adsorption energy for the weak surface adsorption but reduces the adsorption energy for the strong corner adsorption due to increased water-cluster bond length. By analyzing the adsorption induced charge rearrangement through Bader's charge partitioning and electron density difference and the orbital interaction through the projected density of states, we conclude that the bonding between water and gold nanocluster is determined by an interplay between electrostatic interaction and covalent interaction involving both the water lone-pair and in-plane orbitals and the gold 5d and 6s orbitals. Including vdW interaction does not change qualitatively the physical picture but does change quantitatively the adsorption structure due to the fluxionality of gold nanoclusters.     

Characterization of the interface dipole at organic/ metal interfaces

In organics-based (opto)electronic devices, the interface dipoles formed at the organic/metal interfaces play a key role in determining the barrier for charge (hole or electron) injection between the metal electrodes and the active organic layers. The origin of this dipole is rationalized here from the results of a joint experimental and theoretical study based on the interaction between acrylonitrile, a pi-conjugated molecule, and transition metal surfaces (Cu, Ni, and Fe). The adsorption of acrylonitrile on these surfaces is investigated experimentally by photoelectron spectroscopies, while quantum mechanical methods based on density functional theory are used to study the systems theoretically. It appears that the interface dipole formed at an organic/metal interface can be divided into two contributions: (i) the first corresponds to the "chemical" dipole induced by a partial charge transfer between the organic layers and the metal upon chemisorption of the organic molecules on the metal surface, and (ii) the second relates to the change in metal surface dipole because of the modification of the metal electron density tail that is induced by the presence of the adsorbed organic molecules. Our analysis shows that the charge injection barrier in devices can be tuned by modulating various parameters: the chemical potential of the bare metal (given by its work function), the metal surface dipole, and the ionization potential and electron affinity of the organic layer.     

Photochemical Reactions in Self‐Assembled Organic Monolayers Characterized by using Scanning Tunneling Microscopy

Research on the supramolecular self‐assembly behavior at interfaces is of great importance to improving the performance of nanodevices that are based on optical functional materials. In this Minireview, several photoinduced isomerization and polymerization reactions in self‐assembled organic monolayers on surfaces are discussed. Typical organic molecules contain azobenzene, alkynyl, or olefins groups. The feature surface base is a highly oriented pyrolytic graphite (HOPG) surface or a gold surface. Scanning tunneling microscopy (STM) is used as a strong tool to characterize new species’ structures before and after illumination.     

Thin film photochromic materials: Effect of the sol-gel ormosil matrix on the photochromic properties of naphthopyrans

Photochromic naphthopyran derivatives have been embedded in sol-gel prepared organically modified thin films. The introduction of organic functional groups into a silica matrix allows tailoring the surface of its pores and the polarity of the environment of the embedded host molecules. The photochromic properties of the naphthopyran molecules, such as the spectral properties of the coloured forms and the kinetics of the thermal bleaching, depend strongly on the polarity of the pores where the molecules are located and, hence, on the nature and loading of organic functional groups in the composition of the ormosil matrix. Important changes in the photochromic properties of the films have also been induced by modifications in the sol-gel preparation and processing parameters. The photostability of the photochromic molecules upon prolonged exposition to UV light is strongly related to the nature of the embedding ormosil matrix. The introduction of organic functional groups into the inner pore surface of the matrix, where the dye molecules will be located, affects the stability of the molecules, in terms of the effectiveness of the interaction between the photochromic molecules and the pore surface.     

Hierarchical CaCO3 Chromatography: A Stationary Phase Based on Biominerals

In biomineralization, acidic macromolecules play important roles for the growth control of crystals through a specific interaction. Inspired by this interaction, we report on an application of the hierarchical structures in CaCO₃ biominerals to a stationary phase of chromatography. The separation and purification of acidic small organic molecules are achieved by thin‐layer chromatography and flash chromatography using the powder of biominerals as the stationary phase. The unit nanocrystals and their oriented assembly, the hierarchical structure, are suitable for the adsorption site of the target organic molecules and the flow path of the elution solvents, respectively. The separation mode is ascribed to the specific adsorption of the acidic molecules on the crystal face and the coordination of the functional groups to the calcium ions. The results imply that a new family of stationary phase of chromatography can be developed by the fine tuning of hierarchical structures in CaCO₃ materials.     

Spectroscopic diagnostics of organic chemistry in the protostellar environment

A combination of astronomical observations, laboratory studies, and theoretical modelling is necessary to determine the organic chemistry of dense molecular clouds. We present spectroscopic evidence for the composition and evolution of organic molecules in protostellar environments. The principal reaction pathways to complex molecule formation by catalysis on dust grains and by reactions in the interstellar gas are described. Protostellar cores, where warming of dust has induced evaporation of icy grain mantles, are excellent sites in which to study the interaction between gas phase and grain-surface chemistries. We investigate the link between organics that are observed as direct products of grain surface reactions and those which are formed by secondary gas phase reactions of evaporated surface products. Theory predicts observable correlations between specific interstellar molecules, and also which new organics are viable for detection. We discuss recent infrared observations obtained with the Infrared Space Observatory, laboratory studies of organic molecules, theories of molecule formation, and summarise recent radioastronomical searches for various complex molecules such as ethers, azaheterocyclic compounds, and amino acids.