B-Doped Graphdiynes and Several of Their Corresponding Oxides: A Theoretical Study by X-ray Spectra

Boron doping can significantly improve the electronic structure and physical and chemical properties of graphdiyne (GDY), which also expands its application prospects in photoelectricity, catalysis, and biology. The accurate configurations characterization of B-doped graphdiyne (B-GDY) has not been achieved due to insufficient experimental and theoretical research. The current work involves the simulation of the geometries of 11 typical B-GDY and B-doped graphdiyne oxides [B(O)-GDY] as well as a pristine GDY, along with their X-ray photoelectron (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra at the density functional theory (DFT) level. The boron and carbon spectra for various bonding types were theoretically imitated to assess the spectral contributions. Calculated outcomes indicate that there is a noticeable dependence of the NEXAFS spectra on the local structure. The simulated XPS spectra provide precise assignments and an extra supplement to the spectra peaks, in addition to the position and general peak forms of simulated spectral peaks matching the experimental spectra fairly well. The combination of XPS and NEXAFS spectra can give useful information for identifying typical B-GDY and B(O)-GDY molecules. This paper offers a comprehensive structure-spectrum relationship of B-GDY and its oxides as well as a further theoretical prediction and guidance for experimental synthesis, which is helpful to solve the challenging issue of identification of B-doped carbon-based materials.

Theoretic Study of Sulfur-Doped Graphdiynes by X-ray Spectroscopy

Sulfur-doped graphdiyne at different sites has a tremendous impact on its electronic structure and properties. Due to the large number of S-doping sites, there is no comprehensive and systematic experimental and theoretical study regarding the identification of S-doped graphdiyne configurations. In this paper, X-ray photoelectron (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra as well as geometries of 10 sulfur-doped graphdiyne molecules have been simulated at the density functional theory (DFT) level. Different types of carbon spectra were theoretically modeled to analyze the contribution of the spectra. Calculated results show that the NEXAFS spectra exhibit a clear dependence on the local structure. The theoretically simulated XPS spectra are in good agreement with the experimental spectra. The XPS spectra combined with the NEXAFS spectra can provide effective information for identifying the 10 S-doped conformations. Our research results provide further theoretical prediction and guidance for the experimental synthesis of S-doped graphdiyne, which solves the difficult problem of identification of S-doped carbon-based materials.

On the choice of shape and size for truncated cluster-based X-ray spectral simulations of 2D materials

Truncated cluster models represent an effective way for simulating X-ray spectra of 2D materials. Here we systematically assessed the influence of two key parameters, the cluster shape (honeycomb, rectangle, or parallelogram) and size, in X-ray photoelectron (XPS) and absorption (XAS) spectra simulations of three 2D materials at five K-edges (graphene, C 1s; C3N, C/N 1s; h-BN, B/N 1s) to pursue the accuracy limit of binding energy (BE) and spectral profile predictions. Several recent XPS experiments reported BEs with differences spanning 0.3, 1.5, 0.7, 0.3, and 0.3 eV, respectively. Our calculations favor the honeycomb model for stable accuracy and fast size convergence, and a honeycomb with ~10 nm side length (120 atoms) is enough to predict accurate 1s BEs for all 2D sheets. Compared to all these experiments, predicted BEs show absolute deviations as follows: 0.4-0.7, 0.0-1.0, 0.4-1.1, 0.6-0.9, and 0.1-0.4 eV. A mean absolute deviation of 0.3 eV was achieved if we compare only to the closest experiment. We found that the sensitivity of computed BEs to different model shapes depends on systems: graphene, sensitive; C3N, weak; h-BN, very weak. This can be attributed to their more or less delocalized π electrons in this series. For this reason, a larger cluster size is required for graphene than the other two to reproduce fine structures in XAS. The general profile of XAS shows weak dependence to model shape. Our calculations provide optimal parameters and accuracy estimations that are useful for X-ray spectral simulations of general graphene-like 2D materials.

A Raman optical activity spectrometer can sensitively detect lanthanide circularly polarized luminescence

Recently, many studies have appeared in which the Raman optical activity (ROA) instrument was found to be convenient for measuring circularly polarized luminescence (CPL). Typically, weak lanthanide luminescence including circular polarization could be detected. The new detection scheme is referred to as ROA-CPL spectroscopy. It is particularly useful when also the vibrational (ROA) itself is detectable as the molecule structure can be examined more reliably. In this review, development of this chiroptical approach and its applications in structural studies of biomolecules are summarized.

Structural and Spectral Properties of a Nonclassical C66 Isomer with Its Hydrogenated Derivative C66H4 in Theory

X-ray photoelectron and near-edge X-ray absorption fine structure (NEXAFS) spectra, as well as the ground-state electronic/geometrical structures of a newly discovered nonclassical isomer C 2v -C66(NC), and two classical fullerene isomers C 2-#4466C66 and C s -#4169C66 with their hydrogenated derivatives [C 2v -C66H4(NC), C 2-#4466C66H4, and C s -#4169C66H4] have been calculated at the density functional theory (DFT) level. Significant differences were observed in the electronic structures and simulated X-ray spectra after hydrogenation. Simultaneously, both X-ray photoelectron and NEXAFS spectra reflected conspicuous isomer dependence, indicating that the "fingerprints" in the X-ray spectra can offer an effective method for identifying the above-mentioned fullerene isomers. The simulated ultraviolet-visible (UV-vis) absorption spectroscopy of C 2v -C66H4(NC) has also been generated by means of the time-dependent DFT method, and the calculations are well consistent with the experimental results. Consequently, this work reveals that X-ray and UV-vis spectroscopy techniques can provide valuable information to help researchers explore the fullerene electronic structure and isomer identification on the future experimental and theoretical fullerene domains.

Structural and spectral properties of a non-classical C58 isomer and its fluorinated derivatives in theory

The traditional classical fullerene is only composed of pentagons and hexagons, with many different topologies, of which only a few structures conform to the isolated pentagon rule (IPR), which means all five-membered rings are separated by hexagons, whereas isomers that violate the rule are called non-IPR isomers. In contrast, the non-classical fullerene consists of other kinds of polygons such as squares and heptagons in addition to pentagons and hexagons. X-ray photoelectron spectra (XPS), near-edge X-ray absorption fine structure (NEXAFS) spectra and X-ray emission spectra (XES), as well as the ground-state electronic/geometrical structures of the important non-IPR isomers C 3v-#1205C58 and C 2-#1078C58, and the remarkable non-classical isomer C s-C58(NC) with its two fluorides C s-C58(NC)F18(A) and C s-C58(NC)F18(B), have been computed at the density functional theory (DFT) level. Significant differences in the electronic structures and simulated X-ray spectra have been observed after fluorination. Meanwhile, strong isomer dependence has been shown in these spectra, which means the "fingerprint" in the X-ray spectra can effectively identify the above-mentioned fullerene isomers. As a consequence, the work can provide useful information especially isomer identification for experimental and theoretical research in fullerene science.

HERFD-XAS and valence-to-core-XES: new tools to push the limits in research with hard X-rays?

In this perspective, the HERFD-XANES (high energy resolution fluorescence detected X-ray absorption near edge structure) and Kβ2,5- or V2C-XES (valence-to-core X-ray emission spectroscopy) methods are discussed as new and powerful tools for chemical research with hard X-rays. This includes a brief survey of the underlying physical processes and the introduction of experimental issues. The potential of both methods to overcome limitations of conventional XAS (X-ray absorption spectroscopy) and to push the limits for obtaining new information about the electronic and geometric structures of metal centers, in the solid state structure or heterogeneous catalysts, but also in metal complexes and homogeneous catalysts, is discussed by presenting a survey of representative references and recent own studies, rounded off by a conclusion and outlook.

Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity

Accessible values of the φ and ψ torsional angles determining peptide main chain conformation are traditionally displayed in the form of Ramachandran plots. The number of experimental methods making it possible to determine such conformational distribution is limited. In the present study, Raman optical activity (ROA) spectra of Ac-Ala-NHMe were measured and fit by theoretical curves. This revealed the most favored conformers and a large part of the potential energy surface (PES) of this model dipeptide. Such experimental PES compares well to quantum chemical computations, whereas molecular dynamics (MD) modeling reproduces it less faithfully. The surface shape is consistent with the temperature dependence of the spectra, as observed experimentally and predicted by MD. Despite errors associated with spectral modeling and the measurement, the results are likely to facilitate future applications of ROA spectroscopy.

The chemical sensitivity of X-ray spectroscopy: high energy resolution XANES versus X-ray emission spectroscopy of substituted ferrocenes

X-ray spectroscopy at the metal K-edge is an important tool for understanding catalytic processes and provides insight into the geometric and electronic structures of transition metal complexes. In particular, X-ray emission-based methods such as high-energy resolution fluorescence detection (HERFD), X-ray absorption near-edge spectroscopy (XANES) and valence-to-core X-ray emission spectroscopy (V2C-XES) hold the promise of providing increased chemical sensitivity compared to conventional X-ray absorption spectroscopy. Here, we explore the ability of HERFD-XANES and V2C-XES spectroscopy to distinguish substitutions beyond the directly coordinated atoms for the example of ferrocene and selected ferrocene derivatives. The experimental spectra are assigned and interpreted through the use of density functional theory (DFT) calculations. We find that while the pre-edge peaks in the HERFD-XANES spectra are affected by substituents at the cyclopentadienyl ring containing π-bonds [A. J. Atkins, Ch. R. Jacob and M. Bauer, Chem.-Eur. J., 2012, 18, 7021], the V2C-XES spectra are virtually unchanged. The pre-edge in HERFD-XANES probes the weak transition to unoccupied metal d-orbitals, while the V2C-XES spectra are determined by dipole-allowed transitions from occupied ligand orbitals to the 1s core hole. The latter turn out to be less sensitive to changes beyond the first coordination shell.