Many-body analysis and spectroscopic characterization of diazene oligomers: A theoretical study

The present study reports the many-body analysis and spectroscopic characterization of linear and cyclic diazene oligomers in gas and water solvent states. The oligomers of diazene from monomer to pentamer have been considered for the study. The spectroscopic studies such as geometrical parameters, infrared spectra, electronic absorption spectra, and natural transition orbitals (NTOs) were reported. Many-body analysis techniques have been implemented to study the interactions among the diazene oligomers. These calculations have been performed using exchange and correlation functional (B3LYP) and 6-311++G (d,p) basis set. The geometrical parameters and infrared modes of monomer diazene in the gas state are well-matched with the available experimental determinations at this level of theory. A significant change in vibrational modes of linear and cyclic diazene oligomers has been observed in the gas phase-to-water solvent state. The time-dependent density functional theory (TD-DFT) has been used to calculate the electronic absorption spectra of diazene oligomers. The Wavelength of electronic transitions, oscillator strength, and HOMO to LUMO gap has been reported. Many-body analysis shows that two-, three-, four-, and five-body energies have a remarkable contribution to the binding energy in addition to relaxation energies. All these calculations have been performed using Gaussian 16 program package.

Diverse Self-assembly Structures of a Macrocycle Revealed with STM by Adjusting the Solution Concentration

The macrocyclic molecule [3]C₁₂ TT-TPA was synthesized by a Stille coupling reaction through alternately connecting 4,7-bisthienyl-2,1,3-thienothiazole and triphenylamine units. The concentration-dependent self-assembly structures of [3]C₁₂ TT-TPA were explored in liquid/solid interface by scanning tunneling microscopy and density functional theory. After increasing the solution concentration, five different nanostructures were constructed and the molecular packing densities were gradually enhanced. Those structural transformations from loose structures to compact structures are thermodynamically favourable because those transformations are accompanied by the adsorption of more [3]C₁₂ TT-TPA molecules from liquid phase, which increases the interactions between molecules and the interactions between molecules and substrate considerably. This study of fundamental exploration is important to understand the basic formation mechanisms and the stability of two-dimensional functional materials.

Dynamic surface-assisted assembly behaviours mediated by external stimuli

Supramolecular self-assembly behaviors on solid substrates have been widely investigated in the last few decades. Owing to the complexity of interfacial assembly systems, the precise regulation of supramolecular nanostructures is still challenging and waits to be solved. The supramolecular nanostructures are governed by non-covalent bonds, so they can be disrupted and influenced by an external environment. In this review, the dynamic supramolecular nanostructures that are mediated by external stimuli containing guest species, light irradiation, temperature and electric field are discussed in detail. The research studies mentioned in this article are all accomplished by STM, and the effects of these external stimuli on the assembled nanostructures have been elucidated exhaustively here.

Theoretical investigation of the isomerization pathways of diazenes: torsion vs. inversion

Diazenes are an important family of organic compounds used widely in synthetic and materials chemistry. These molecules have a planar geometry and exhibit cis-trans isomerization. The simplest of all these molecules - diazene (N2H2) - has been subjected to several experimental and theoretical studies. Two mechanisms have been proposed for the cis-trans isomerization of diazene, which are an in-plane inversion and an out-of-plane torsion. The activation energies for these pathways are similar and the competition between these two mechanisms has been discussed in the literature based on electronic structure theory calculations. Three decades ago, a classical dynamics investigation of diazene isomerization was carried out using a model Hamiltonian and it was indicated that the in-plane inversion is forbidden classically because of a centrifugal barrier and the out-of-plane torsion is the only isomerization pathway. In the present work, we investigated the cis-trans isomerization dynamics of diazene using ab initio classical trajectory simulations at the CASSCF(2,2)/aug-cc-pVDZ level of electronic structure theory. The simulation results confirmed the presence of the aforementioned centrifugal barrier for the inversion and torsion was the only observed pathway. The calculations were repeated for a similar system (difluorodiazene, N2F2) and again the centrifugal barrier prevented the inversion pathway.

Mechanism of Chain Polymerization in Self-Assembled Monolayers of Diacetylene on the Graphite Surface

We have studied the mechanism of photoinduced chain polymerization in the self-assembled monolayer of a diacetylene compound, 10,12-pentacosadiyn-1-ol, on the graphite surface. We statistically analyze the polymerization degree of the polydiacetylene chains formed at different temperatures using scanning tunneling microscopy. The distributions of the polymerization degree agree well with the prediction from a simple probabilistic model, allowing for addition reaction and deactivation at both the ends of the chain as stochastic events. The estimated activation energies of the addition reaction and deactivation are noticeably different from those of the conventional solid-state polymerization in the bulk crystals of diacetylene.

Reversible Photoisomerization of Monolayers of π-Expanded Oligothiophene Macrocycles at Solid-Liquid Interfaces

Self‐assembled monolayers of a π‐expanded oligothiophene macrocycle undergo photoisomerization between their Z,Z and E,E diastereomers at the interface between octanoic acid solutions and highly oriented pyrolytic graphite (HOPG). The switching process proceeds in situ at the solid–liquid interface and was followed by scanning tunneling microscopy (STM). Upon illumination with light at 365 nm (546 nm), a monolayer of Z,Z‐8mer (E,E‐8mer) photoisomerizes to the E,E‐8mer (Z,Z‐8mer) form with changes in 2D hexagonal packing. These findings provide insight towards the design of photoresponsive surfaces with desirable optoelectronic and structural (host–guest) properties.

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.

Adsorption-geometry induced transformation of self-assembled nanostructures of an aldehyde molecule on Cu(110)

From an interplay of high-resolution STM imaging/manipulation and DFT calculations, we have revealed that different self-assembled nanostructures of BA molecules on Cu(110) are attributable to specific molecular adsorption geometries, and thus the corresponding intermolecular hydrogen bonding patterns. The STM manipulations demonstrate the feasibility of switching such weak-hydrogen-bonding patterns.

Two-dimensional solid-state topochemical reactions of 10,12-pentacosadiyn-1-ol adsorbed on graphite

The photoinduced topochemical reaction of the diacetylene (DA) compound 10,12-pentacosadiyn-1-ol in the two-dimensional (2D) crystal phase adsorbed on graphite was examined by scanning tunneling microscopy (STM). The reaction efficiency and the structure of the generated polydiacetylene depend on its polymorphic forms, i.e., the "herringbone" or the "parallel" monomer arrangements. The reaction efficiency of the herringbone arrangement is lower than that of the parallel arrangement because the distance R between the probable reactant acetylenic carbon atoms of the herringbone arrangement is longer than that of the parallel arrangement. However, the fact that polydiacetylenes form from the herringbone arrangement (R = 0.58 nm) is contrary to the geometric criteria for the polymerization of three-dimensional (3D) crystals (the reaction was only observed if R < 0.4 nm). The polymerization criterion for the 2D phase differs from that of the 3D phase. In addition, the STM cross-section profiles of the polydiacetylenes reveal that the "lifted-up" and "in-plane" conformations form from the parallel and herringbone arrangements, respectively.

Two-dimensional self-assemblies of telechelic organic compounds: structure and surface host-guest chemistry

Guiding the self-assembly of different types of functional molecules into well-defined structures on surfaces is beneficial for both fundamental surface and interface study and emerging application fields, especially molecular and organic electronics. This review focuses on understanding the two-dimensional self-assembly process of telechelic organics, which feature alkoxylene chains terminated with carboxyl groups. With the combined flexibility of alkyl chains and directionality of carboxyl groups, telechelic organics show unique assembly behaviour on two-dimensional surfaces. By increasing the length of the alkoxylene chains, the cavities in the nanoporous networks of telechelic trimesic acid (1,3,5-benzene tricarboxylic acid) derivatives change from hexagonal cavities to irregular cavities on a highly oriented pyrolytic graphite surface. The nanoporous networks provide a flexible host template for host-guest supramolecular chemistry because the cavities framed by the flexible alkoxylene chains can be changed in accordance with the sizes/shapes of the guest molecules. Furthermore, the terminal carboxylic group can form a hydrogen bond with another hydrogen bond partner, leading to multi-component structural motifs and hierarchical assemblies. The unique assembly behaviour of telechelic organics makes them promising structures as important building blocks for the design and construction of complex self-assembled nanoarchitectures.

Optically and thermally induced molecular switching processes at metal surfaces

Using light to control the switching of functional properties of surface-bound species is an attractive strategy for the development of new technologies with possible applications in molecular electronics and functional surfaces and interfaces. Molecular switches are promising systems for such a route, since they possess the ability to undergo reversible changes between different molecular states and accordingly molecular properties by excitation with light or other external stimuli. In this review, recent experiments on photo- and thermally induced molecular switching processes at noble metal surfaces utilizing two-photon photoemission and surface vibrational spectroscopies are reported. The investigated molecular switches can either undergo a trans-cis isomerization or a ring opening-closure reaction. Two approaches concerning the connection of the switches to the surface are applied: physisorbed switches, i.e. molecules in direct contact with the substrate, and surface-decoupled switches incorporated in self-assembled monolayers. Elementary processes in molecular switches at surfaces, such as excitation mechanisms in photoisomerization and kinetic parameters for thermally driven reactions, which are essential for a microscopic understanding of molecular switching at surfaces, are presented. This in turn is needed for designing an appropriate adsorbate-substrate system with the desired switchable functionality controlled by external stimuli.

Interfacial self-assembly of amino acids and peptides: scanning tunneling microscopy investigation

Proteins play important roles in human daily life. To take advantage of the lessons learned from nature, it is essential to investigate the self-assembly of subunits of proteins, i.e., amino acids and polypeptides. Due to its high resolution and versatility of working environment, scanning tunneling microscopy (STM) has become a powerful tool for studying interfacial molecular assembly structures. This review is intended to reflect the progress in studying interfacial self-assembly of amino acids and peptides by STM. In particular, we focus on environment-induced polymorphism, chiral recognition, and coadsorption behavior with molecular templates. These studies would be highly beneficial to research endeavors exploring the mechanism and nanoscale-controlling molecular assemblies of amino acids and polypeptides on surfaces, understanding the origin of life, unravelling the essence of disease at the molecular level and deeming what is necessary for the "bottom-up" nanofabrication of molecular devices and biosensors being constructed with useful properties and desired performance.

Supramolecular assembly/reassembly processes: molecular motors and dynamers operating at surfaces

Among the many significant advances within the field of supramolecular chemistry over the past decades, the development of the so-called "dynamers" features a direct relevance to materials science. Defined as "combinatorial dynamic polymers", dynamers are constitutional dynamic systems and materials resulting from the application of the principles of supramolecular chemistry to polymer science. Like supramolecular materials in general, dynamers are reversible dynamic multifunctional architectures, capable of modifying their constitution by exchanging, recombining, incorporating components. They may exhibit a variety of novel properties and behave as adaptive materials. In this review we focus on the design of responsive switchable monolayers, i.e. monolayers capable to undergo significant changes in their physical or chemical properties as a result of external stimuli. Scanning tunneling microscopy studies provide direct evidence with a sub-nanometre resolution, on the formation and dynamic response of these self-assembled systems featuring controlled geometries and properties.

Engineering of linear molecular nanostructures by a hydrogen-bond-mediated modular and flexible host-guest assembly

The formation of a desired nanostructure with concomitant patterns and functions is of utmost importance in the field of surface molecular engineering and nanotechnology. We here present a flexible host-guest assembly, which steers the formation of linear molecular nanostructures on surfaces by a hydrogen-bond-mediated assembly process. A linear monodendron molecular template with periodic hydrogen-bond binding sites is shown to accommodate a variety of molecules with pyridylethynyl terminals. The unit cell parameters in the transverse direction of the linear pattern can be tuned from 3.4 to 7.3 nm in response to the packing of the guest molecules with different sizes, shapes, and aggregation number. The introduction of hydrogen-bonding partners into the host template and into guest molecules is responsible for the steering of the linear pattern of guest molecules. The modular approach could greatly facilitate the ordering of guest molecules with desired functional moieties.

Adamantane-Based Tripodal Thioether Ligands Functionalized with a Redox-Active Ferrocenyl Moiety for Self-Assembled Monolayers

Self-assembled monolayers (SAMs) can decorate surfaces with `smart´ functional units possessing reversible stimulus-response behavior for optical, thermal, magnetic or redox-chemical stimuli. An independent performance of individual functional groups in such a film is desirable, which can be, in particular, ensured by fairly large lateral separations between tailgroups in the SAM. Adsorbate molecules with multiple attachment points are very promising in this context owing to their large surface footprint, which covers a surface area exceeding the lateral dimensions of the functional groups. To address these design constraints, novel tridentate long-chain tripodal thioether ligands with central adamantine units and a redox-active ferrocenyl tailgroup, 1-[4-(ferrocenylethynyl)phenyl]-3,5,7-tri[(4-n-octylsulfanyl)phenyl]adamantine (T8) and 1-[4-(ferrocenylethynyl)phenyl]-3,5,7-tri[(4-n-dodecylsulfanyl)phenyl]adamantine (T12), were synthesized and used as tripodal adsorbate molecules for the fabrication of redox-active ferrocenyl-terminated SAMs on Au(111). These SAMs were characterized by X-ray photoelectron spectroscopy, near edge X-ray absorption fine structure spectroscopy and sum frequency generation spectroscopy. The data suggest that T8 and T12 form almost contamination-free, well-aligned and fairly densely-packed SAMs on Au(111) with laterally separated ferrocenyl units. The SAMs show a homogeneous binding chemistry, an important requirement for high fidelity SAMs. SFG results indicate lateral interactions between neighboring molecules via the long-chain binding units.

An electron induced two-dimensional switch made of azobenzene derivatives anchored in supramolecular assemblies

Supramolecular assemblies of 4-anilino-4'-nitroazobenzene are investigated on the Au(111) surface by low temperature scanning tunneling microscopy and spectroscopy with submolecular resolution. Adsorption at 250 K leads to three different structures that are formed via hydrogen bonds: a star structure and two types of line structures: a meandering and a zigzag line. The formation of these supramolecular assemblies is affected by the available space on the fcc domains of the reconstructed Au(111) substrate as well as by the two-dimensional chirality of the molecules on the surface. The star structure is enantiomerically pure, while both types of lines consist of a racemic mixture. Bonding between homochiral pairs differ from the one between heterochiral pairs in the position of the hydrogen bonds. Inside these supramolecular assemblies two configurations of the molecules are identified: An almost straight trans-configuration and a slightly bent cis*-configuration. The trans-configuration largely reflects the structure of this isomer in gas phase, while the cis*-configuration is two-dimensional on the surface in contrast to the three-dimensional gas phase cis-configuration. The reversible trans-cis* isomerization is induced by electron tunneling through the LUMO+1 state of the molecule, which is located at +2.9 V.

COOH-terminated SAMs on gold fabricated from an azobenzene derivative with a 1,2-dithiolane headgroup

Well-defined and homogeneous, contamination-free self-assembled monolayers (SAMs) were fabricated by the chemisorption of lip-NH-p-C₆H₄-N=N-p-C₆H₄-COOH (lip = α-lipoyl) onto gold. This adsorbate species is composed of a 1,2-dithiolane-based headgroup, an azobenzene-based (and hence photochromic) spacer unit and a carboxylic acid functional group. The SAM constituents are covalently attached to the substrate by the bidentate thiolate anchor groups and exhibit a strongly tilted binding configuration.

Accurate ab initio based DMBE potential energy surface for the ground electronic state of N2H2

A global single-sheeted double many-body expansion potential energy surface is reported for the ground electronic state of N(2)H(2). Starting from an approximate cluster expansion of the molecular potential that utilizes previously reported functions of the same family for the triatomic fragments, four-body energy terms have been calibrated from extensive accurate ab initio data so as to reproduce the main features of the title system. The switching function formalism previously suggested for three-body systems [A. J. C. Varandas and L. Poveda, Theor. Chem. Acc. 116, 404 (2006)] has been generalized to approximate the true multisheeted nature of N(2)H(2) potential energy surface, thus allowing the correct behavior at the N((2)D) + NH(2)((2)A(")) and N((4)S) + NH(2)((4)A(")) dissociation limits. The resulting fully six-dimensional potential energy function reproduces the correct symmetry under permutation of identical atoms and predicts the main stationary points of the molecule in the valence and long-range regions in good agreement with available experimental and theoretical data on the diazene molecule.