Impact of Halogen Termination and Chain Length on π-Electron Conjugation and Vibrational Properties of Halogen-Terminated Polyynes.

We explored the optoelectronic and vibrational properties of a new class of halogen-terminated carbon atomic wires in the form of polyynes using UV-vis, infrared absorption, Raman spectroscopy, X-ray single-crystal diffraction, and DFT calculations. These polyynes terminate on one side with a cyanophenyl group and on the other side, with a halogen atom X (X = Cl, Br, I). We focus on the effect of different halogen terminations and increasing lengths (i.e., 4, 6, and 8 sp-carbon atoms) on the π-electron conjugation and the electronic structure of these systems. The variation in the sp-carbon chain length is more effective in tuning these features than changing the halogen end group, which instead leads to a variety of solid-state architectures. Shifts between the vibrational frequencies of samples in crystalline powders and in solution reflect intermolecular interactions. In particular, the presence of head-to-tail dimers in the crystals is responsible for the modulation of the charge density associated with the π-electron system, and this phenomenon is particularly important when strong I··· N halogen bonds occur.

Thiophene-Based Conjugated Acetylenic Polymers with Dual Active Sites for Efficient Co-Catalyst-Free Photoelectrochemical Water Reduction in Alkaline Medium.

Although being attractive materials for photoelectrochemical hydrogen evolution reaction (PEC HER) under neutral or acidic conditions, conjugated polymers still show poor PEC HER performance in alkaline medium due to the lack of water dissociation sites. Herein, we demonstrate that tailoring the polymer skeleton from poly(diethynylthieno[3,2-b]thiophene) (pDET) to poly(2,6-diethynylbenzo[1,2-b:4,5-b']dithiophene (pBDT) and poly(diethynyldithieno[3,2-b:2',3'-d]thiophene) (pDTT) in conjugated acetylenic polymers (CAPs) introduces highly efficient active sites for water dissociation. As a result, pDTT and pBDT, grown on Cu substrate, demonstrate benchmark photocurrent densities of 170 µA cm-2 and 120 µA cm-2 (at 0.3 V vs. RHE; pH 13), which are 4.2 and 3 times higher than that of pDET, respectively. Moreover, by combining DFT calculations and electrochemical operando resonance Raman spectroscopy, we propose that the electron-enriched Cß of the outer thiophene rings of pDTT are the water dissociation active sites, while the -C≡C- bonds function as the active sites for hydrogen evolution.

Solvent-dependent termination, size and stability in polyynes synthesized via laser ablation in liquids.

In recent years there has been growing interest in sp-carbon chains as possible novel nanostructures. An example of sp-carbon chains is the so-called polyyne, characterized by the alternation of single and triple bonds that can be synthesized via pulsed laser ablation in liquid (PLAL) of a graphite target. In this work, by using different solvents in the PLAL process, e.g. water, acetonitrile, methanol, ethanol, and isopropanol, we systematically investigated the role of the solvent in polyyne synthesis and stability, and discussed the possible formation mechanisms. The presence of methyl- and cyano-groups in the solutions influences the termination of polyynes, allowing the detection, of hydrogen-capped polyynes up to H-C22-H, methyl-capped polyynes up to H-C18-CH3 and cyanopolyynes up to H-C12-CN. The assignment of each species was performed via UV-vis spectroscopy and supported by density functional theory simulations of vibronic spectra. In addition, surface-enhanced Raman spectroscopy allowed to highlight the differences in the shape and positions of the characteristic Raman bands of the size-selected polyynes with different terminations (hydrogen, methyl and cyano groups). The stability in time of each polyyne was investigated by evaluating the chromatographic peak area, and the effect of size, terminations and solvents on polyyne stability was individuated.

Thiabendazole and Thiabendazole-Formic Acid Solvate: A Computational, Crystallographic, Spectroscopic and Thermal Study.

Thiabendazole (TBZ) is a substance which has been receiving multiple important applications in several domains, from medicine and pharmaceutical sciences, to agriculture and food industry. Here, a comprehensive multi-technique investigation on the molecular and crystal properties of TBZ is reported. In addition, a new solvate of the compound is described and characterized structurally, vibrationally and thermochemically for the first time. Density functional theory (DFT) calculations were used to investigate the conformational space of thiabendazole (TBZ), revealing the existence of two conformers, the most stable planar trans form and a double-degenerated-by-symmetry gauche form, which is ~30 kJ mol-1 higher in energy than the trans conformer. The intramolecular interactions playing the major roles in determining the structure of the TBZ molecule and its conformational preferences were characterized. The UV-visible and infrared spectra of the isolated molecule (most stable trans conformer) were also calculated, and their assignment undertaken. The information obtained for the isolated molecule provided a strong basis for the understanding of the intermolecular interactions and properties of the crystalline compound. In particular, the infrared spectrum for the isolated molecule was compared with that of crystalline TBZ and the differences between the two spectra were interpreted in terms of the major intermolecular interactions existing in the solid state. The analysis of the infrared spectral data was complemented with vibrational results of up-to-date fully-periodic DFT calculations and Raman spectroscopic studies. The thermal behavior of TBZ was also investigated using differential scanning calorimetry (DSC) and thermogravimetry. Furthermore, a new TBZ-formic acid solvate [2-(1,3-thiazol-4-yl)benzimidazolium formate formic acid solvate] was synthesized and its crystal structure determined by X-ray diffraction. The Hirshfeld method was used to explore the intermolecular interactions in the crystal of the new TBZ solvate, comparing them with those present in the neat TBZ crystal. Raman spectroscopy and DSC studies were also carried out on the solvate to further characterize this species and investigate its temperature-induced desolvation.

Bottom-Up Synthesis of Heteroatom-Doped Chiral Graphene Nanoribbons.

Bottom-up synthesis of graphene nanoribbons (GNRs) has significantly advanced during the past decade, providing various GNR structures with tunable properties. The synthesis of chiral GNRs, however, has been underexplored and only limited to (3,1)-GNRs. We report herein the surface-assisted synthesis of the first heteroatom-doped chiral (4,1)-GNRs from the rationally designed precursor 6,16-dibromo-9,10,19,20-tetraoxa-9a,19a-diboratetrabenzo[ a, f, j, o]perylene. The structure of the chiral GNRs has been verified by scanning tunneling microscopy, noncontact atomic force microscopy, and Raman spectroscopy in combination with theoretical modeling. Due to the presence of oxygen-boron-oxygen (OBO) segments on the edges, lateral self-assembly of the GNRs has been observed, realizing well-aligned GNR arrays with different modes of homochiral and heterochiral inter-ribbon assemblies.

Intermolecular modulation of IR intensities in the solid state. The role of weak interactions in polyethylene crystal: A computational DFT study.

Density functional theory calculations with periodic boundary conditions are exploited to study the infrared spectrum of crystalline polyethylene. Spectral changes lead by the intermolecular packing in the orthorhombic three-dimensional crystal are discussed by means of a careful comparison with calculations carried out for an isolated polymer chain in the all-trans conformation, described as an ideal one-dimensional crystal. The results are analyzed in the framework of the "oligomer approach" through the modelling of the IR spectrum of n-alkanes of different lengths. The study demonstrates that a relevant absorption intensity modulation of CH2 deformation transitions takes place in the solid state. This finding suggests a new interpretation for the experimental evidences collected in the past by means of IR intensity measurement during thermal treatment. Moreover, the comparison between calculations for 3-D crystal and for the isolated polyethylene chain (1-D crystal) allows to put in evidence the effect of the local electric field on the computed infrared intensities. This observation provides guidelines for the comparison between infrared absorption intensities predicted for an isolated unit and for a molecule belonging to a crystal, through the introduction of suitable correction factors based on the refraction index of the material and depending on the dimensionality of such units (0D-molecule; 1D-polymer; 2D-slab).

Structure and vibrational properties of 1D molecular wires: from graphene to graphdiyne.

Graphyne- and graphdiyne-like model systems have attracted much attention from many structural, theoretical, and synthetic scientists because of their promising electronic, optical, and mechanical properties, which are crucially affected by the presence, abundance and distribution of triple bonds within the nanostructures. In this work, we performed the two-step bottom-up on-surface synthesis of graphyne- and graphdiyne-based molecular wires on the Au(111). We characterized their structural and chemical properties both in situ (UHV conditions) through STM and XPS and ex situ (in air) through Raman spectroscopy. By comparing the results with the well-known growth of poly(p-phenylene) wires (namely the narrowest armchair graphene nanoribbon), we were able to show how to discriminate different numbers of triple bonds within a molecule or a nanowire also containing phenyl rings. Even if the number of triple bonds can be effectively determined from the main features of STM images and confirmed by fitting the C1s peak in XPS spectra, we obtained the most relevant results from ex situ Raman spectroscopy, despite the sub-monolayer amount of molecular wires. The detailed analysis of Raman spectra, combined with density functional theory (DFT) simulations, allowed us to identify the main features related to the presence of isolated (graphyne-like systems) or at least two conjugated triple bonds (graphdiyne-like systems). Moreover, other spectral features can be exploited to understand if the chemical structure of graphyne- and graphdiyne-based nanostructures suffered unwanted reactions. As in the case of sub-monolayer graphene nanoribbons obtained by on-surface synthesis, we demonstrate that Raman spectroscopy can be used for a fast, highly sensitive and non-destructive determination of the properties, the quality and the stability of the graphyine- and graphdiyne-based nanostructures obtained by this highly promising approach.

Charge mobility in molecules: charge fluxes from second derivatives of the molecular dipole.

On the basis of the analytical model previously suggested by Dinur, we discuss here a method for the calculation of vibrational charge fluxes in planar molecules, obtained as numerical second derivatives of the molecular dipole moment. This model is consistent with the partitioning of the atomic polar tensors into atomic charge and charge fluxes according to the Equilibrium Charges-Charge Fluxes model and it is directly related to experimentally measurable quantities such as IR intensities. On the basis of density functional theory calculations carried out for several small benchmark molecules, the complete set of charge fluxes is calculated for each molecule and compared with the approximated flux parameters previously derived and reported in the past literature. The degree of localization of charge fluxes is investigated and discussed; in addition, some approximations are analyzed in order to verify the applicability of the method to large and∕or non-planar molecules, aimed at obtaining a description of the electron charge mobility in different molecular environments.

Infrared intensities and charge mobility in hydrogen bonded complexes.

The analytical model for the study of charge mobility in the molecules presented by Galimberti et al. [J. Chem. Phys. 138, 164115 (2013)] is applied to hydrogen bonded planar dimers. Atomic charges and charge fluxes are obtained from density functional theory computed atomic polar tensors and related first derivatives, thus providing an interpretation of the IR intensity enhancement of the X-H stretching band observed upon aggregation. Our results show that both principal and non-principal charge fluxes have an important role for the rationalization of the spectral behavior; moreover, they demonstrate that the modulation of the charge distribution during vibrational motions of the -XH⋯Y- fragment is not localized exclusively on the atoms directly involved in hydrogen bonding. With these premises we made some correlations between IR intensities, interaction energies, and charge fluxes. The model was tested on small dimers and subsequently to the bigger one cytosine-guanine. Thus, the model can be applied to complex systems.

A pressure-polishing set-up to fabricate patch pipettes that seal on virtually any membrane, yielding low access resistance and efficient intracellular perfusion.

When performing whole-cell configuration recordings, it is important to minimize series resistance to reduce the time constant of charging the cell membrane capacitance and to reduce error in membrane potential control. To this end, an existing method was improved by widening the patch pipette shank through the calibrated combination of heat and air pressure. The heat was produced by passing current through a filament that was shaped appropriately to ensure a homogeneous heating of the pipette shank. Pressurized air was applied to the lumen of a pipette, pulled from a borosilicate glass microcap, via the pressure port of a modified commercial holder. The pipette reshaping was viewed on an LCD monitor connected to a contrast-intensified CCD camera and coupled to a modified bright-field stereomicroscope. By appropriately regulating the timing of air pressure and the application of heating, the pipette shank and, independently, the tip opening diameter were widened as desired. The methods illustrated here to fabricate and use the patch pipettes, using just one glass type, allowed the sealing of a wide variety of cell types isolated from different amphibian, reptilian, fish, and mammalian tissues as well as a variety of artificial membranes made with many different lipid mixtures. The access resistance yielded by pressure-polished pipettes was approximately one-fourth the size of the one attained with conventional pipettes; besides improving the electrical recordings, this minimized intracellular ion accumulation or depletion as well. Enlarged shank geometry allowed for fast intracellular perfusion as shown by fluorescence imaging, also via pulled quartz or plastic tubes, which could be inserted very close to the pipette tip.

Photogenerated cumulenic structure of adamantyl endcapped linear carbon chains: an experimental and computational investigation based on infrared spectroscopy.

The infrared (IR) spectrum of an adamantyl endcapped α, ω-polyyne (the hexayne, Ad-C(12)-Ad) is investigated both experimentally and computationally. A new IR band is observed upon UV photoexcitation of the compound (embedded in a poly methyl methacrylate matrix at 78 K), thus, revealing the existence of new photogenerated molecular structure trapped at low temperature. Complete reversibility is found, thus, demonstrating that the photoexcitation is responsible for the generation of metastable excited states of the molecule. Density functional theory and time dependent density functional theory calculations indicate that these metastable states result from the forbidden singlet (S(1)) or triplet (T(1)) excited states, and geometry optimizations of the polyyne trapped in either S(1) and/or T(1) states demonstrate that the carbon chain takes on a cumulenic structure. Comparison of the experimental and the computed IR spectra for the molecule trapped in the forbidden states confirms that the new IR features are clear markers of cumulenic species. The temperature and time dependent behavior of the new IR band is analyzed, while the experimentally determined value of the activation energy highlights the low stability of these molecular structures.

Designing All Graphdiyne Materials as Graphene Derivatives: Topologically Driven Modulation of Electronic Properties.

Designing new 2D systems with tunable properties is an important subject for science and technology. Starting from graphene, we developed an algorithm to systematically generate 2D carbon crystals belonging to the family of graphdiynes (GDYs) and having different structures and sp/sp2 carbon ratios. We analyze how structural and topological effects can tune the relative stability and the electronic behavior, to propose a rationale for the development of new systems with tailored properties. A total of 26 structures have been generated, including the already known polymorphs such as α-, ß-, and γ-GDY. Periodic density functional theory calculations have been employed to optimize the 2D crystal structures and to compute the total energy, the band structure, and the density of states. Relative energies with respect to graphene have been found to increase when the values of the carbon sp/sp2 ratio increase, following however different trends based on the peculiar topologies present in the crystals. These topologies also influence the band structure, giving rise to semiconductors with a finite band gap, zero-gap semiconductors displaying Dirac cones, or metallic systems. The different trends allow identifying some topological effects as possible guidelines in the design of new 2D carbon materials beyond graphene.

Modeling of molecular charge distribution on the basis of experimental infrared intensities and first-principles calculations: the case of CH bonds.

DFT calculations are used to predict CH stretching infrared (IR) intensities for about 50 small molecules. B3LYP and PBE1PBE functionals and different basis sets are tested to obtain the best agreement with the experimental absolute IR intensities available. PBE1PBE functional in particular predicts average CH stretching intensities very close to the experimental ones. On the basis of a simple analytical model, it is shown how it is possible to extract atomic charges directly from computed atomic polar tensors (APTs): these IR charges are very close in value to the experimentally derived ones and faithfully reproduce peculiar molecular phenomena. DFT-derived IR charges are also compared with the charges obtained by population schemes such as Mulliken population analysis, natural population analysis (NPA), and with charges obtained by fitting the electrostatic potential according to the Merz-Kollman (MK), CHELP, and CHELPG models. IR charges are found to be similar especially to the charges obtained by these last methods: therefore they can be used as an alternative scheme for the determination of the molecular charge distribution while being strictly connected to experimentally measurable properties. Moreover, the analytical model is further developed to obtain a method for the calculation of the charge fluxes, which take place along the chemical bonds during molecular vibrations.

A Field-Effect Transistor Based on Cumulenic sp-Carbon Atomic Wires.

Carbyne and linear carbon structures based on sp-hybridization are attractive targets as the ultimate one-dimensional system (i.e., one-atom in diameter) featuring wide tunability of optical and electronic properties. Two possible structures exist for sp-carbon atomic wires: (a) the polyynes with alternated single-triple bonds and (b) the cumulenes with contiguous double bonds. Theoretical studies predict semiconducting behavior for polyynes, while cumulenes are expected to be metallic. Very limited experimental work, however, has been directed toward investigating the electronic properties of these structures, mostly at the single-molecule or monolayer level. However, sp-carbon atomic wires hold great potential for solution-processed thin-film electronics, an avenue not exploited to date. Herein, we report the first field-effect transistor (FET) fabricated employing cumulenic sp-carbon atomic wires as a semiconductor material. Our proof-of-concept FET device is easily fabricated by solution drop casting and paves the way for exploiting sp-carbon atomic wires as active electronic materials.

Structural, Electronic, and Vibrational Properties of a Two-Dimensional Graphdiyne-like Carbon Nanonetwork Synthesized on Au(111): Implications for the Engineering of sp-sp2 Carbon Nanostructures.

Graphdiyne, atomically thin two-dimensional (2D) carbon nanostructure based on sp-sp2 hybridization is an appealing system potentially showing outstanding mechanical and optoelectronic properties. Surface-catalyzed coupling of halogenated sp-carbon-based molecular precursors represents a promising bottom-up strategy to fabricate extended 2D carbon systems with engineered structure on metallic substrates. Here, we investigate the atomic-scale structure and electronic and vibrational properties of an extended graphdiyne-like sp-sp2 carbon nanonetwork grown on Au(111) by means of the on-surface synthesis. The formation of such a 2D nanonetwork at its different stages as a function of the annealing temperature after the deposition is monitored by scanning tunneling microscopy (STM), Raman spectroscopy, and combined with density functional theory (DFT) calculations. High-resolution STM imaging and the high sensitivity of Raman spectroscopy to the bond nature provide a unique strategy to unravel the atomic-scale properties of sp-sp2 carbon nanostructures. We show that hybridization between the 2D carbon nanonetwork and the underlying substrate states strongly affects its electronic and vibrational properties, modifying substantially the density of states and the Raman spectrum compared to the free standing system. This opens the way to the modulation of the electronic properties with significant prospects in future applications as active nanomaterials for catalysis, photoconversion, and carbon-based nanoelectronics.

Pore forming properties of cecropin-melittin hybrid peptide in a natural membrane.

The pore forming properties of synthetic cecropin-melittin hybrid peptide (Acetyl-KWKLFKKIGAVLKVL-CONH(2); CM15) were investigated by using photoreceptor rod outer segments (OS) isolated from frog retinae obtained by using the whole-cell configuration of the patch-clamp technique. CM15 was applied (and removed) to (from) the OS in approximately 50 ms with a computer-controlled microperfusion system. Once the main OS endogenous conductance was blocked with light, the OS membrane resistance was >or=1 G Omega, allowing high resolution, low-noise recordings. Different to alamethicines, CM15 produced voltage-independent membrane permeabilisation, repetitive peptide application caused a progressive permeabilisation increase, and no single-channel events were detected at low peptide concentrations. Collectively, these results indicate a toroidal mechanism of pore formation by CM15.

Molecular dynamics investigation of halogenated amyloidogenic peptides.

Besides their biomolecular relevance, amyloids, generated by the self-assembly of peptides and proteins, are highly organized structures useful for nanotechnology applications. The introduction of halogen atoms in these peptides, and thus the possible formation of halogen bonds, allows further possibilities to finely tune the amyloid nanostructure. In this work, we performed molecular dynamics simulations on different halogenated derivatives of the ß-amyloid peptide core-sequence KLVFF, by using a modified AMBER force field in which the σ-hole located on the halogen atom is modeled with a positively charged extra particle. The analysis of equilibrated structures shows good agreement with crystallographic data and experimental results, in particular concerning the formation of halogen bonds and the stability of the supramolecular structures. The modified force field described here allows describing the atomistic details contributing to peptides aggregation, with particular focus on the role of halogen bonds. This framework can potentially help the design of novel halogenated peptides with desired aggregation propensity. Graphical abstract Molecular dynamics investigation of halogenated amyloidogenic peptides.

Scanning tunneling microscopy and Raman spectroscopy of polymeric sp-sp2 carbon atomic wires synthesized on the Au(111) surface.

Long linear carbon nanostructures based on sp-hybridization can be synthesized by exploiting on-surface synthesis of halogenated precursors evaporated on Au(111), thus opening a way to investigations by surface-science techniques. By means of an experimental approach combining scanning tunneling microscopy and spectroscopy (STM and STS) with ex situ Raman spectroscopy we investigate the structural, electronic and vibrational properties of polymeric sp-sp2 carbon atomic wires composed by sp-carbon chains connected through phenyl groups. Density-functional-theory (DFT) calculations of the structure and the electronic density of states allow us to simulate STM images and to compute Raman spectra. The comparison of experimental data with DFT simulations unveil the properties and the formation stages as a function of the annealing temperature. Atomic-scale structural information from STM complement the Raman sensitivity to the single molecular bond to open the way to detailed understanding of these novel carbon nanostructures.

The effect of intermolecular dipole-dipole interaction on Raman spectra of polyconjugated molecules: density functional theory simulations and mathematical models.

In this work, we analyze the effect of intermolecular dipole-dipole interactions on Raman spectra of polyconjugated molecules. In particular, the behavior of push-pull polyenes has been studied. By means of density functional theory (DFT) calculations on isolated molecules and dimers, we have found that both the frequencies and intensities of the strongest Raman lines (R mode) are strongly influenced by intermolecular interactions. The results have been rationalized within the effective conjugation coordinate (ECC) theory developed in the past. The calculations for different configurations have also shown that the Raman spectra are sensible to different intermolecular geometries, thus implying a possible application of vibrational spectroscopy to the study of supramolecular properties of polyconjugated systems. The comparison with the available experimental spectra confirms the results obtained with the DFT computations. Finally, a very simple mathematical model is proposed for the prediction of the Raman frequencies of interacting systems. From the knowledge of just a few quantities for the isolated molecule and of some geometrical parameters, an estimate of the frequency of the dimers can be obtained. Despite its simplicity, this model gives results in very good agreement with DFT calculations carried out explicitly on dimers in several different arrangements.

A halogen bond-donor amino acid for organocatalysis in water.

Herein we report a halogen bond-donor amino acid, 4-iodotetrafluorophenylalanine, which behaves as a catalyst for the aqueous synthesis of bis-(heterocyclic)methanes. We also provide experimental evidence that halogen bonding is a plausible explanation for the observed catalytic effect.