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.

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.

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.

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.

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.

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.

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.

Fingerprints of sp¹ Hybridized C in the Near-Edge X-ray Absorption Spectra of Surface-Grown Materials.

Carbon structures comprising sp 1 chains (e.g., polyynes or cumulenes) can be synthesized by exploiting on-surface chemistry and molecular self-assembly of organic precursors, opening to the use of the full experimental and theoretical surface-science toolbox for their characterization. In particular, polarized near-edge X-ray absorption fine structure (NEXAFS) can be used to determine molecular adsorption angles and is here also suggested as a probe to discriminate sp 1 /sp 2 character in the structures. We present an ab initio study of the polarized NEXAFS spectrum of model and real sp 1 /sp 2 materials. Calculations are performed within density functional theory with plane waves and pseudopotentials, and spectra are computed by core-excited C potentials. We evaluate the dichroism in the spectrum for ideal carbynes and highlight the main differences relative to typical sp 2 systems. We then consider a mixed polymer alternating sp 1 C 4 units with sp 2 biphenyl groups, recently synthesized on Au(111), as well as other linear structures and two-dimensional networks, pointing out a spectral line shape specifically due to the the presence of linear C chains. Our study suggests that the measurements of polarized NEXAFS spectra could be used to distinctly fingerprint the presence of sp 1 hybridization in surface-grown C structures.

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.

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.

Copper-surface-mediated synthesis of acetylenic carbon-rich nanofibers for active metal-free photocathodes.

The engineering of acetylenic carbon-rich nanostructures has great potential in many applications, such as nanoelectronics, chemical sensors, energy storage, and conversion, etc. Here we show the synthesis of acetylenic carbon-rich nanofibers via copper-surface-mediated Glaser polycondensation of 1,3,5-triethynylbenzene on a variety of conducting (e.g., copper, graphite, fluorine-doped tin oxide, and titanium) and non-conducting (e.g., Kapton, glass, and silicon dioxide) substrates. The obtained nanofibers (with optical bandgap of 2.51 eV) exhibit photocatalytic activity in photoelectrochemical cells, yielding saturated cathodic photocurrent of ca. 10 µA cm-2 (0.3-0 V vs. reversible hydrogen electrode). By incorporating thieno[3,2-b]thiophene units into the nanofibers, a redshift (ca. 100 nm) of light absorption edge and twofold of the photocurrent are achieved, rivalling those of state-of-the-art metal-free photocathodes (e.g., graphitic carbon nitride of 0.1-1 µA cm-2). This work highlights the promise of utilizing acetylenic carbon-rich materials as efficient and sustainable photocathodes for water reduction.

Domino Reaction for the Sustainable Functionalization of Few-Layer Graphene.

The mechanism for the functionalization of graphene layers with pyrrole compounds was investigated. Liquid 1,2,5-trimethylpyrrole (TMP) was heated in air in the presence of a high surface area nanosized graphite (HSAG), at temperatures between 80 °C and 180 °C. After the thermal treatments solid and liquid samples, separated by centrifugation, were analysed by means of Raman, Fourier Transform Infrared (FT-IR) spectroscopy, X-Rays Photoelectron Spectroscopy (XPS) and ¹H-Nuclear Magnetic Resonance (¹H NMR) spectroscopy and High Resolution Transmission Electron Microscopy (HRTEM). FT-IR spectra were interpreted with the support of Density Functional Theory (DFT) quantum chemical modelling. Raman findings suggested that the bulk structure of HSAG remained substantially unaltered, without intercalation products. FT-IR and XPS spectra showed the presence of oxidized TMP derivatives on the solid adducts, in a much larger amount than in the liquid. For thermal treatments at T ≥ 150 °C, IR spectral features revealed not only the presence of oxidized products but also the reaction of intra-annular double bond of TMP with HSAG. XPS spectroscopy showed the increase of the ratio between C(sp²)N bonds involved in the aromatic system and C(sp³)N bonds, resulting from reaction of the pyrrole moiety, observed while increasing the temperature from 130 °C to 180 °C. All these findings, supported by modeling, led to hypothesize a cascade reaction involving a carbocatalyzed oxidation of the pyrrole compound followed by Diels-Alder cycloaddition. Graphene layers play a twofold role: at the early stages of the reaction, they behave as a catalyst for the oxidation of TMP and then they become the substrate for the cycloaddition reaction. Such sustainable functionalization, which does not produce by-products, allows us to use the pyrrole compounds for decorating sp² carbon allotropes without altering their bulk structure and smooths the path for their wider application.

Combining Static and Dynamical Approaches for Infrared Spectra Calculations of Gas Phase Molecules and Clusters.

Four models for the calculation of the IR spectrum of gas phase molecules and clusters from molecular dynamics simulations are presented with the aim to reduce the computational cost of the usual Fourier transform (FT) of the time correlation function of the dipole moment. These models are based on the VDOS, FT of time correlation function of velocities, and atomic polar tensors (APT). The models differ from each other by the number of APTs inserted into the velocities correlation function. Excellent accuracy is achieved by the model adopting a weighted linear combination of a few selected APTs adapted for the rotation of the molecule (model D). The achieved accuracy relates to band positions, band shapes, and band intensities. Depending on the degree of actual dynamics of the molecule, rotational motion, conformational isomerization, and large amplitude motions that can be seen during the finite temperature trajectory, one could also apply one of the other models (models A, B, or C), but with caution. Model D is therefore found simple and accurate, with appealing computational cost and should be systematically applied. Its generalization to condensed phase systems should be straightforward.

Static vs dynamic DFT prediction of IR spectra of flexible molecules in the condensed phase: The (ClCF2CF(CF3)OCF2CH3) liquid as a test case.

First-principles molecular dynamics (FPMD) simulations in the framework of Density Functional Theory (DFT) are carried out for the prediction of the infrared spectrum of the fluorinated molecule ClCF2CF(CF3)OCF2CH3 in liquid and gas phase. This molecule is characterized by a flexible structure, allowing the co-existence of several stable conformers, that differ by values of the torsional angles. FPMD computed spectra are compared to the experimental ones, and to Boltzmann weighted IR spectra based on gas phase calculations.

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).

Vibrational Response of Methylammonium Lead Iodide: From Cation Dynamics to Phonon-Phonon Interactions.

The dynamic evolution of the vibrational interactions in the prototypical CH3 NH3 PbI3 was studied through a comprehensive experimental and theoretical investigation with a focus on the interactions between the organic cations and the inorganic cage. To date, no clear picture has emerged on the critical and fundamental interactions between the two perovskite components, despite the relevance of phonons to the electronic properties of several classes of perovskites. For the first time, we have monitored the IR and nonresonant Raman response in the broad frequency range 30-3400 cm-1 and in the temperature interval 80-360 K. Strong changes in the energies of different vibrational modes with temperature are observed and examined in the framework of phonon-phonon interactions considering a significant anharmonic contribution to the phonon relaxation process. The vibrational relaxation of the bending modes and their reorientation activation energies identify that such mechanisms are governed by medium-to-strong hydrogen bonds in the orthorhombic phase; however, any ferroelectric ordering in the orthorhombic phase is governed mostly by dipole interactions. These changes imply that charge localization mechanisms play a primary role, and our study enriches the fundamental knowledge of phonon interactions and charge transport in CH3 NH3 PbI3 for the further development of optoelectronic applications.

Joint experimental and computational investigation of the structural and spectroscopic properties of poly(vinylidene fluoride) polymorphs.

State-of-the-art density functional theory calculations are here adopted for the investigation of the crystal structure and of the vibrational properties of α, ß, γ, and δ phases of poly(vinylidene fluoride) (PVDF), in comparison with IR and Raman measurements. DFT calculations allowed a detailed interpretation of the IR and Raman spectra of α and ß phases, giving vibrational assignments useful for qualitative and quantitative characterization of these systems. From a molecular perspective, the computational investigation of the crystal structure and the spectra of PVDF polymorphs helped in clarifying the role of supramolecular dipole-dipole interactions, which indeed modulate the vibrational properties of these systems, indicating also that intermolecular interaction could play a significant role in the modulation of ferroelectric properties. Furthermore, the combined experimental and computational approach allowed us to identify and characterize the thermally and mechanically induced γ phase, shedding light on the far-IR marker bands of this elusive phase of PVDF.