DFT vibrational calculations of rhodamine 6G adsorbed on silver: analysis of tip-enhanced Raman spectroscopy

The tip-enhanced near-field Raman (TERS) bands of Rhodamine 6G (R6G), that we reported earlier [Chem. Phys. Lett. 2001, 335, 369.], are assigned on the basis of density-functional theory (DFT) calculations at the 6-311++G(d,p) level. The Raman and infrared intensities as well as frequencies of the vibrational modes are used for band assignments. These vibrational modes, in combination with characterization of resonant electronic transitions using time-dependent DFT calculations, predict spectral changes in resonant Raman and surface-enhanced resonant Raman scatterings of R6G. Moreover, the TERS spectra of R6G are analyzed in detail, where interactions between the tip and R6G molecules and their enhancement mechanisms are discussed. Finally, we propose a novel Raman spectroscopy technique capable of detecting molecular vibrations at sub-nanometer scale.     

Protein-ligand binding investigated by a single nanoparticle TERS approach

We report TERS imaging of individual 50 nm, biotin-labeled gold nanoparticles bound to a streptavidin-derivatized glass slide. Individual gold nanoparticles detected by a nanoparticle TERS tip generate Raman enhancements in both the biotin and streptavidin signals. These results indicate that nanoparticles are capable of investigating nanoscale spatial and chemical environments with non-resonant Raman enhancements.     

β‐Iminoenamine‐BF2 Complexes: Aggregation‐Induced Emission and Pronounced Effects of Aliphatic Rings on Radiationless Deactivation

The synthesis, photophysical, and electrochemical attributes of a novel class of boron difluorides containing an aromatic‐fused alicyclic/hetero‐alicyclic ring built on a β‐iminoenamine chromophoric backbone are reported. The compounds displayed large Stokes shifts (86–121 nm), and were emissive in the solid state. The quantum yields obtained in solution at room temperature were unusually lower by an order of magnitude compared to those in the solid state. Some of the tested compounds displayed aggregation‐induced emission (AIE). Single crystal XRD analyses revealed a lack of interplanar π–π interactions, which are presumed to be absent owing to non‐planarity of the alicyclic component in the molecule. For most of the studied compounds, time‐dependent DFT (TD‐DFT) calculations invariably reveal intramolecular charge transfer (π–π*) characteristics with the frontier orbitals concentrated on the boron–nitrogen heterocycle. The participation of boron and fluorine atoms was found to be negligible.     

Study on the Film Properties and Recognition for Metal Ions of Calix[4]arenes Derivative by Langmuir Monolayer

Calixarene molecules are very powerful ligand for ions and small molecules, and have been studied with several techniques as models for host‐guest systems. In this approach, the formation of Langmuir monolayer properties of three kinds calix[4]arene derivative were characterized and one of them, p‐tert‐butylthiacalix[4]arene (TCA), was chosen as object to study its Langmuir monolayer affected by different subphase conditions. The purpose of this study is to investigate the molecular recognition ability of TCA for metal ions at the water‐air interface. Changing the composition of aqueous subphase (containing various metal ion solutions respectively) produced strong variations on the monolayer parameters, indicating a different selectivity of the TCA ligand for the different metal cations. In particular, high selectivity for transition metal ions was found. Limiting area values are discussed in relation to the orientation of the cone‐shaped molecules at the water‐air interface.     

Molecular Characterization of DNA Double Strand Breaks with Tip‐Enhanced Raman Scattering

DNA double strand breaks (DSBs) are deadly lesions that can lead to genetic defects and cell apoptosis. Techniques that directly detect DNA DSBs include scanning electron microscopy, atomic force microscopy (AFM), and fluorescence based approaches. While these techniques can be used to identify DSBs they provide no information on the molecular events occurring at the break. Tip‐enhanced Raman scattering (TERS) can provide molecular information from DNA at the nanoscale and in combination with AFM provides a new way to visualize and characterize the molecular structure of DSBs. DSBs result from cleavage at the 3’‐ and 5’‐bonds of deoxyribose upon exposure to UVC radiation based on the observation of P? O? H and methyl/methylene deformation modes enhanced in the TERS spectra. It is hypothesized that strand fragments are hydrogen‐terminated at the lesion, indicating the action of free radicals during photon exposure.     

Singly and Doubly 1,2‐Phenylene‐Inserted Porphyrin Arch‐Tape Dimers: Synthesis and Highly Contorted Structures

Singly and doubly 1,2‐phenylene‐inserted Ni^II porphyrin arch‐tape dimers 3 and 9 were synthesized from the corresponding β‐to‐β 1,2‐phenylene‐bridged Ni^II porphyrin dimers 5 and 11 via Ni⁰‐mediated reductive cyclization and DDQ/Sc(OTf)₃‐promoted oxidative cyclization as key steps, respectively. Owing to the fused eight‐membered ring(s), 3 showed a more contorted structure than those of previously reported arch‐tape dimers 2 a and 2 b possessing a fused seven‐membered ring. Furthermore, 9 displayed much larger molecular contortion. As the molecular contortion increases, the Q band of the absorption spectrum becomes more red‐shifted and the electrochemcial HOMO–LUMO gap becomes smaller, reaching at 1294 nm and 0.77 eV in 9 , respectively. The effect of molecular contortion on the electronic properties was studied by means of DFT calculations.     

Multichannel Conductance of Folded Single‐Molecule Wires Aided by Through‐Space Conjugation

Deciphering charge transport through multichannel pathways in single‐molecule junctions is of high importance to construct nanoscale electronic devices and deepen insight into biological redox processes. Herein, we report two tailor‐made folded single‐molecule wires featuring intramolecular π–π stacking interactions. The scanning tunneling microscope (STM) based break‐junction technique and theoretical calculations show that through‐bond and through‐space conjugations are integrated into one single‐molecule wire, allowing for two simultaneous conducting channels in a single‐molecule junction. These folded molecules with stable π–π stacking interaction offer conceptual advances in single‐molecule multichannel conductance, and are perfect models for conductance studies in biological systems, organic thin films, and π‐stacked columnar aggregates.     

Protonated primary amines induced thymine quintets studied by electrospray ionization mass spectrometry and density functional theory calculations

As the novel magic number clusters of nucleobases, the thymine quintets induced by ammonium ion (NH₄⁺), and particularly by its derivatives such as protonated alkyl amines and protonated aryl amines, have been studied by electrospray ionization mass spectrometry (ESI‐MS) and density functional theory (DFT) calculations. The DFT‐optimized geometry of NH₄⁺ induced thymine quintet ([T₅ + NH₄]⁺) reveals some new features including three additional hydrogen bonds between NH₄⁺ and its surrounding thymine molecules when compared with that of the alkali metal ions induced thymine quintets. In addition, the fourth hydrogen atom of NH₄⁺ is sticking out the assembly, and, thus, it might be replaced by an organic group R to form the protonated primary amine induced thymine quintet ([T₅ + R ? NH₃]⁺), a hypothesis that has been confirmed by both DFT calculations and ESI‐MS experiments. Furthermore, the relative abilities of the different protonated primary amines for inducing the thymine quintets are investigated by ESI‐MS competition experiments, and the results have shown a clear trend of stronger ability as the alkyl chain gets longer or as the aryl ring gets larger for the alkyl amines or the aryl amines. Two basic influence factors are consequently identified: one is the ability of the alkyl amine to accept proton, another is the π–π stacking interaction between the aryl ring and the π‐surface of the thymine molecule(s), whose explanations are strongly supported by multiple types of thermochemical data, various control experiments and DFT calculations. Copyright © 2014 John Wiley & Sons, Ltd.     

Structural Characterization of a Covalent Monolayer Sheet Obtained by Two‐Dimensional Polymerization at an Air/Water Interface

This work describes a two‐dimensional polymerization at an air/water interface and provides, for the first time, direct spectroscopic evidence for the kind of crosslinks formed and for the conversion reached in a covalently bonded monolayer sheet. This evidence was obtained through a combination of a variety of monolayer characterization techniques before and after transfer onto solid substrates, in particular by tip‐enhanced Raman spectroscopy (TERS) and TERS mapping after transfer of both the monomer and polymer monolayer onto Au(111). This work is a major advance for the field of 2D polymers synthesized at the air/water interface as it, in principle, allows estimation of the crystallinity by percolation theory and the location of regions with defects.     

Exciton‐Vibrational Couplings in Homo‐ and Heterodimer Stacks of Perylene Bisimide Dyes within Cyclophanes: Studies on Absorption Properties and Theoretical Analysis

The optical properties of a series of three cyclophanes comprising either identical or different perylene bisimide (PBI) chromophores were studied by UV/Vis absorption spectroscopy and their distinctive spectral features were analyzed. All the investigated cyclophanes show significantly different absorption features with respect to the corresponding constituent PBI monomers indicating strong coupling interactions between the PBI units within the cyclophanes. DFT calculations suggest a π‐stacked arrangement of the PBI units at close van der Waals distance in the cyclophanes with rotational displacement. Simulations of the absorption spectra based on time‐dependent quantum mechanics properly reproduced the experimental spectra, revealing exciton‐vibrational coupling between the chromophores both in homo‐ and heterodimer stacks. The PBI cyclophane comprising two different PBI chromophores represents the first example of a PBI heterodimer stack for which the exciton coupling has been investigated. The quantum dynamics analysis reveals that exciton coupling in heteroaggregates is indeed of similar strength as for homoaggregates.     

Benzotrithiophene versus Benzo/Naphthodithiophene Building Blocks: The Effect of Star‐Shaped versus Linear Conjugation on Their Electronic Structures

The synthesis, characterization, and optical properties of a novel star‐shaped oligothiophene with a central rigid trithienobenzene (BTT) core and diketopyrrolopyrrole (DPP) units are reported and compared with homologous linear systems based on the benzodithiophene (BDT) and the naphthodithiophene (NDT) units end capped with DPPs. This comparison is aimed at elucidating the effect of the star‐shaped configuration versus linear conformation on the optical and electrical properties. Electronic and vibrational spectroscopies, together with transient absorption spectroscopy, scanning electronic microscopy, and DFT calculations are used to understand not only the molecular properties of these semiconductors, but also to analyze the supramolecular aggregation in these derivatives. We conclude that although the subject star‐shaped derivative is not optimal in terms of π‐conjugation, its extended BTT unit significantly favors intermolecular π‐stacking interactions, which is interesting for their applications in devices. Field‐effect transistors and solar cells were fabricated with these new molecular semiconductors and the performance difference discussed.     

Dissecting the concave–convex π‐π interaction in corannulene and sumanene dimers: SAPT(DFT) analysis and performance of DFT dispersion‐corrected methods

The characteristics of the concave–convex π‐π interactions are evaluated in 32 buckybowl dimers formed by corannulene, sumanene, and two substituted sumanenes (with S and CO groups), using symmetry‐adapted perturbation theory [SAPT(DFT)] and density functional theory (DFT). According to our results, the main stabilizing contribution is dispersion, followed by electrostatics. Regarding the ability of DFT methods to reproduce the results obtained with the most expensive and rigorous methods, TPSS‐D seems to be the best option overall, although its results slightly tend to underestimate the interaction energies and to overestimate the equilibrium distances. The other two tested DFT‐D methods, B97‐D2 and B3LYP‐D, supply rather reasonable results as well. M06‐2X, although it is a good option from a geometrical point of view, leads to too weak interactions, with differences with respect to the reference values amounting to about 4 kcal/mol (25% of the total interaction energy). © 2017 Wiley Periodicals, Inc.     

Towards chemical analysis of nanostructures in biofilms II: tip-enhanced Raman spectroscopy of alginates

This study examines the feasibility of using tip-enhanced Raman spectroscopy (TERS) for label-free chemical characterization of nanostructures in biological systems. For this purpose, a well-defined model system consisting of calcium alginate fibers is studied. In a companion paper, calcium alginate fibers and their network structures were shown to be a good model for the extracellular polysaccharides of biofilms at the nanoscale. TERS analysis of biological macromolecules, such as alginates, is complicated by heterogeneity in their sequence, molecular weight, and conformations, their small Raman cross-section, and the large number of functional groups, which can chemically interact with the silver surface of the tip and cause significant band shifts. Due to these effects, Raman frequencies in TERS spectra of biopolymers do not necessarily resemble band positions in the normal Raman spectrum of the bulk material, as is the case for less complex samples (e.g., dye molecules) studied so far. Additionally, analyte decomposition due to laser heating can have a significant influence, and carbon contamination signals can sometimes even overwhelm the weak analyte signals. Based on the investigation of alginates, strategies for spectra correction, choice of appropriate reference samples, and data interpretation are presented. With this approach, characteristic frequency ranges and specific marker bands can be found for biological macromolecules that can be employed for their identification in complex environments. Figure TERS spectrum of a calcium alginate fiber bundle     

The choice of appropriate density functional for the calculation of static first hyperpolarizability of azochromophores and stacking dimers

The effect of the stacked azo‐chromophore dimer formation on the values of static first hyperpolarizability is studied in the framework of the DFT‐based approach; calculations were also performed at the MP2 level. A number of dispersion‐corrected density functionals—В97D, ωВ97X‐D, and M06‐2X—is tested to calculate the structure of the dimer, the value of binding energy, and molecular nonlinear optical characteristics. According to the QTAIM analysis, the presence of bond critical points is revealed in the intermolecular region, the signs and values of topological characteristics giving evidence for the noncovalent van der Waals interaction between the chromophores. The formation of stacks results in moderate increase of dimer static first hyperpolarizability as compared to that of a single chromophore, the effect depending on the relative shift of the chromophores in dimer. In a special case of greatly shifted chromophores, this enhancement of the first hyperpolarizability becomes appreciable and achieves 72%. © 2015 Wiley Periodicals, Inc.     

Nanoscale Chemical Imaging Using Tip‐Enhanced Raman Spectroscopy: A Critical Review

Methods for chemical analysis at the nanometer scale are crucial for understanding and characterizing nanostructures of modern materials and biological systems. Tip‐enhanced Raman spectroscopy (TERS) combines the chemical information provided by Raman spectroscopy with the signal enhancement known from surface‐enhanced Raman scattering (SERS) and the high spatial resolution of atomic force microscopy (AFM) or scanning tunneling microscopy (STM). A metallic or metallized tip is illuminated by a focused laser beam and the resulting strongly enhanced electromagnetic field at the tip apex acts as a highly confined light source for Raman spectroscopic measurements. This Review focuses on the prerequisites for the efficient coupling of light to the tip as well as the shortcomings and pitfalls that have to be considered for TERS imaging, a fascinating but still challenging way to look at the nanoworld. Finally, examples from recent publications have been selected to demonstrate the potential of this technique for chemical imaging with a spatial resolution of approximately 10 nm and sensitivity down to the single‐molecule level for applications ranging from materials sciences to life sciences.     

Dehydrocoupling and Silazane Cleavage Routes to Organic–Inorganic Hybrid Polymers with NBN Units in the Main Chain

Despite the great potential of both π‐conjugated organoboron polymers and BN‐doped polycyclic aromatic hydrocarbons in organic optoelectronics, our knowledge of conjugated polymers with B?N bonds in their main chain is currently scarce. Herein, the first examples of a new class of organic–inorganic hybrid polymers are presented, which consist of alternating NBN and para‐phenylene units. Polycondensation with B?N bond formation provides facile access to soluble materials under mild conditions. The photophysical data for the polymer and molecular model systems of different chain lengths reveal a low extent of π‐conjugation across the NBN units, which is supported by DFT calculations. The applicability of the new polymers as macromolecular polyligands is demonstrated by a cross‐linking reaction with Zr^IV.     

Fabrication of a Biocompatible Mica/Gold Surface for Tip-Enhanced Raman Spectroscopy

Tip-enhanced Raman spectroscopy (TERS) is a promising technique for structural studies of biological systems and biomolecules, owing to its ability to provide a chemical fingerprint with sub-diffraction-limit spatial resolution. This application of TERS has thus far been limited, due to difficulties in generating high field enhancements while maintaining biocompatibility. The high sensitivity achievable through TERS arises from the excitation of a localized surface plasmon resonance in a noble metal atomic force microscope (AFM) tip, which in combination with a metallic surface can produce huge enhancements in the local optical field. However, metals have poor biocompatibility, potentially introducing difficulties in characterizing native structure and conformation in biomolecules, whereas biocompatible surfaces have weak optical field enhancements. Herein, a novel, biocompatible, highly enhancing surface is designed and fabricated based on few-monolayer mica flakes, mechanically exfoliated on a metal surface. These surfaces allow the formation of coupled plasmon enhancements for TERS imaging, while maintaining the biocompatibility and atomic flatness of the mica surface for high resolution AFM. The capability of these substrates for TERS is confirmed numerically and experimentally. We demonstrate up to five orders of magnitude improvement in TERS signals over conventional mica surfaces, expanding the sensitivity of TERS to a wide range of non-resonant biomolecules with weak Raman cross-sections. The increase in sensitivity obtained through this approach also enables the collection of nanoscale spectra with short integration times, improving hyperspectral mapping for these applications. These mica/metal surfaces therefore have the potential to revolutionize spectromicroscopy of complex, heterogeneous biological systems such as DNA and protein complexes.     

Cyclophanes Containing Bowl‐Shaped Aromatic Chromophores: Three Isomers of anti‐[2.2](1,4)Subphthalocyaninophane

The connection of bowl‐shaped aromatic boron subphthalocyanines with anti‐[2.2]paracyclophane resulted in the first observation of electronic communication between convex and concave surfaces. Three isomers of anti‐[2.2](1,4)subphthalocyaninophane, described as concave–concave ( CC ), convex–concave ( CV ), and convex–convex ( VV ) according to the orientation of the subphthalocyanine units, were synthesized and characterized by various spectroscopic techniques, including ¹H NMR, electronic absorption, fluorescence, and magnetic circular dichroism spectroscopy and X‐ray crystallography, together with molecular‐orbital calculations. On going from the CC system to CV and further to VV , the Q band broadened and finally split as a result of through‐space expansion of the conjugated systems, which were also reproduced theoretically.     

Vibrational Property of α-Borophene Determined by Tip-Enhanced Raman Spectroscopy

We report a Raman characterization of the α borophene polymorph by scanning tunneling microscopy combined with tip-enhanced Raman spectroscopy. A series of Raman peaks were discovered, which can be well related with the phonon modes calculated based on an asymmetric buckled α structure. The unusual enhancement of high-frequency Raman peaks in TERS spectra of α borophene is found and associated with its unique buckling when landed on the Ag(111) surface. Our paper demonstrates the advantages of TERS, namely high spatial resolution and selective enhancement rule, in studying the local vibrational properties of materials in nanoscale.     

The impact of basis set superposition error on the structure of π?π dimers

The effect of basis set superposition error (BSSE) on the structure and energy of benzene, naphthalene, corannulene, and sumanene dimer has been analyzed. MP2 method was chosen and the effect is estimated using 6‐31G, 6‐31G(d), 6‐311+G(d), cc‐pVDZ, and cc‐pVTZ basis sets. The model calculations on benzene dimer indicate that the impact of BSSE on the equilibrium geometry of π‐stacked dimers appears to be quite significant. Calculations on larger molecular dimers such as the dimers of naphthalene, corannulene, and sumanene are also studied. The practical implication of the current observation on modeling the macromolecular structure is discussed. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011