Exploring large O 1s and N 1s core level shifts due to intermolecular hydrogen bond formation in organic molecules

García-Gil, Sandra; Arnau, A.; García-Lekue, Aran

doi:10.1016/j.susc.2013.03.017

Cited by 26 publications

(23 citation statements)

References 37 publications

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“…Such findings fully corroborate our previous conclusions simply derived by observing the energy difference between the experimental IE and BE, ∆(IE-BE), of the two N 1s levels. Similar results were also observed in the theoretical study of Garcia-Gil et al [51], where, through the screening of several H-bonded molecular structures, they found the BE of the H-donor to be much more affected compared to that of the H-acceptor. By increasing the number of melamine units, i.e.…”

Section: Expsupporting

confidence: 88%

Spectroscopic Fingerprints of Intermolecular H‐Bonding Interactions in Carbon Nitride Model Compounds

Lanzilotto

Silva

Zhang

et al. 2018

Chemistry A European J

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The effect of intermolecular H-bonding interactions on the local electronic structure of N-containing functional groups (amino group and pyridine-like N) that are characteristic of polymeric carbon nitride materials p-CN(H), a new class of metal-free organophotocatalysts, was investigated. Specifically, the melamine molecule, a building block of p-CN(H), was characterized by X-ray photoelectron (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The molecule was studied as a noninteracting system in the gas phase and in the solid state within a H-bonded network. With the support of DFT simulations of the spectra, it was found that the H-bonds mainly affect the N 1s level of the amino group, leaving the N 1s level of the pyridine-like N mostly unperturbed. This is responsible for a reduction of the chemical shift between the two XPS N 1s levels relative to free melamine. Consequently, N K-edge NEXAFS resonances involving the amino N 1s level also shift to lower photon energies. Moreover, the solid-state absorption spectra showed significant modification/quenching of resonances related to transitions from the amino N 1s level to σ* orbitals involving the NH termini.

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Section: Expsupporting

confidence: 88%

Spectroscopic Fingerprints of Intermolecular H‐Bonding Interactions in Carbon Nitride Model Compounds

Lanzilotto

Silva

Zhang

et al. 2018

Chemistry A European J

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“…In the 2,2′-bipyridine system, the non-protonated CN nitrogen is involved in a long, intramolecular bridging CN···H−N + (between the two 2,2′-nitrogen atoms, d(N−H) 2.189 Å), 35 as opposed to the shorter intermolecular CN···H−O in 4BPY/sulfo (d(N−H) 1.461 Å, Supporting Information), and variation in hydrogen bonding interactions can lead to small decreases in energy of this magnitude. 14,24,25,49 Closer inspection of the N 1s binding energies and N 1s → 1π* energies for the CN nitrogen of the co-crystals shows a small yet successively higher energy occurs with a shorter distance between the H-bonded acceptor nitrogen of 4,4′-bipyridine and hydrogen of the acid molecule (N···H−O, Figure 6, Table 1). Indeed, there is a term in the potential model for XPS relating to atomic distances in addition to charge, 50 and there are initial computational results indicative of a dependence of core level energy on hydrogen bond distances for oxygen.…”

Section: ■ Discussionmentioning

confidence: 99%

Proton Transfer, Hydrogen Bonding, and Disorder: Nitrogen Near-Edge X-ray Absorption Fine Structure and X-ray Photoelectron Spectroscopy of Bipyridine–Acid Salts and Co-crystals

Stevens

Newton

Jaye

et al. 2015

Crystal Growth & Design

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The sensitivity of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to Brønsted donation and the protonation state of nitrogen in the solid state is investigated through a series of multicomponent bipyridine− acid systems alongside X-ray photoelectron spectroscopy (XPS) data. A large shift to high energy occurs for the 1s → 1π* resonance in the nitrogen K-edge NEXAFS with proton transfer from the acid to the bipyridine base molecule and allows assignment as a salt (CNH + ), with the peak ratio providing the stoichiometry of the types of nitrogen species present. A corresponding binding energy shift for CNH + is observed in the nitrogen XPS, clearly identifying protonation and formation of a salt. The similar magnitude shifts observed with both techniques relative to the unprotonated nitrogen of co-crystals (CN) suggest that the chemical state (initial-state) effects dominate. Results from both techniques reveal the sensitivity to identify proton transfer, hydrogen bond disorder, and even the potential to distinguish variations in hydrogen bond length to nitrogen. ■ INTRODUCTIONProton (hydrogen) transfer can be thought of as one of the simplest chemical reactions, ranging from complete transfer from an acidic to a basic moiety (protonation through Brønsted donation) to varying degrees of sharing through hydrogen bonding. Whether Brønsted proton transfer occurs has a profound effect on the location of protons in crystal structures and influences chemical and physical properties. These interactions can be employed to target properties of solid forms (crystal engineering), with particular relevance to the pharmaceutical industry where acid/base guest molecules can be combined with active ingredients to tailor properties such as solubility and bioavailability through formation of salts and cocrystals. 1−4 Other relevant fields are organic ferroelectrics, 5 energetic materials, 6 and the design of materials with targeted optical properties such as color 7 and luminescence. 8,9 Even among hydrogen bonds, the level of interaction with the donor and acceptor atoms can vary significantly, from relatively weak to strong with quasi-covalent character, 10 and there is also the possibility of disordered hydrogen bonds. 11 While X-ray diffraction (XRD) and solid-state nuclear magnetic resonance spectroscopy (ssNMR) are often techniques of choice for structural characterization, 2,11−14 they are not always unambiguous with regard to proton locations (although further clarity can often be obtained by neutron diffraction). 11,13−16 The importance of accurate characterization of salts vs co-crystals based on this relatively small difference in proton location should not be underestimated, particularly with the wider implications for intellectual property and regulatory control in the pharmaceutical industry. 4,17 X-ray photoelectron spectroscopy (XPS) has recently been shown to unequivocally identify whether intermolecular proton transfer occurs in a range of two-component systems and distinguish protonation (salt...

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“…The implemented methodology has been used to study, for example, the shifts induced by hydrogen bonding in organic molecules 156 .…”

Section: Core Level Shiftsmentioning

confidence: 99%

Siesta: Recent developments and applications

Garcı́a

Papior

Akhtar

et al. 2020

The Journal of Chemical Physics

283

210

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A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-nineties, SIESTA's flexibility, efficiency and free distribution has given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudoatomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here we describe the more recent implementations on top of that core scheme, which include: full spin-orbit interaction, non-repeated and multiple-contact ballistic electron transport, DFT+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, densityfunctional perturbation theory, efficient Van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as WANNIER90 and the second-principles modelling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various postprocessing utilities. SIESTA has also been a) Electronic mail:

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Exploring large O 1s and N 1s core level shifts due to intermolecular hydrogen bond formation in organic molecules

Cited by 26 publications

References 37 publications

Spectroscopic Fingerprints of Intermolecular H‐Bonding Interactions in Carbon Nitride Model Compounds

Spectroscopic Fingerprints of Intermolecular H‐Bonding Interactions in Carbon Nitride Model Compounds

Proton Transfer, Hydrogen Bonding, and Disorder: Nitrogen Near-Edge X-ray Absorption Fine Structure and X-ray Photoelectron Spectroscopy of Bipyridine–Acid Salts and Co-crystals

Siesta: Recent developments and applications

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