Correlation of electronic structures of three cyclic dipeptides with their photoemission spectra

Dehydrogenation of Ammonia Borane Impacts Valence and Core Electrons: A Photoemission Spectroscopic Study

Ammonia borane (H₃BNH₃) is a promising material for hydrogen storage and release. Dehydrogenation of ammonia borane produces small boron-nitrogen hydrides such as aminoborane (H₂BNH₂) and iminoborane (HBNH). The present study investigates ammonia borane and its two dehydrogenated products for the first time using calculated photoemission spectra of the valence and core electrons. It is found that a significant decrease in the dipole moment was observed associated with the dehydration from 5.397 D in H₃BNH₃, to 1.942 D in H₂BNH₂, and to 0.083 D in HBNH. Such reduction in the dipole moment impacts properties such as hydrogen bonding, dihydrogen bonding, and their spectra. Dehydrogenation of H₃BNH₃ impacts both the valence and core electronic structure of the boron-nitrogen hydrides. The calculated valence vertical ionization energy (VIE) spectra of the boron-nitrogen hydrides show that valence orbitals dominated by 2p-electrons of B and N atoms exhibit large changes, whereas orbitals dominated by s-electrons, such as (3a₁4a₁5a₁/3σ4σ5σ) remain less affected. The first ionization energy slightly increases from 10.57 eV for H₃BNH₃ to 11.29 eV for both unsaturated H₂BNH₂ and HBNH. In core space, the oxidative dehydrogenation of H₃BNH₃ affects the core electron binding energy (CEBE) of borane and nitrogen oppositely. The B1s binding energies increase from 194.01 eV in H₃BNH₃ to 196.93 eV in HBNH, up by 2.92 eV, whereas the N1s binding energies decrease from 408.20 eV in H₃BNH₃ to 404.88 eV in HBNH, dropped by 3.32 eV.

Photoelectron-photoion(s) coincidence studies of molecules of biological interest

Photoelectron-photoion(s) coincidence, PEPICO, experiments with synchrotron radiation have become one of the most powerful tools to investigate dissociative photoionization thanks to their selectivity. In this paper their application to the study of molecular species of biological interest in the gas phase is reviewed. Some applications of PEPICO to the study of potential radiosensitizers, amino acids and small peptides and opportunities offered by the advent of novel methods for the production of beams of these molecules are discussed.

Electron and ion spectroscopy of the cyclo-alanine-alanine dipeptide

The VUV photoionisation and photofragmentation of cyclo-alanine-alanine (cAA) has been studiedin a joint experimental and theoretical work. The photoelectron spectrum and the photoelectron-photoion coincidence (PEPICO) measurements, which enable a control...

A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase

The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations. Then, different first principles computational schemes are considered to simulate the spectra: Hartree-Fock (HF), density functional theory (DFT) within the B3LYP approximation, the quasi-particle GW correction, and the quantum-chemistry CCSD method. Theory allows assignment of the main features of the spectra. A discussion on the role of electronic correlation is provided, by comparing computationally cheaper DFT scheme (and GW) results with the accurate CCSD method.

Two-Dimensional Coordination Networks from Cyclic Dipeptides

Peptide-based biomimetic nanostructures and metal-organic coordination networks on surfaces are two promising classes of hybrid materials which have been explored recently. However, despite the great versatility and structural variability of natural and synthetic peptides, the two directions have so far not been merged in fabrication of metal-organic coordination networks using peptides as building blocks. Here we demonstrate that cyclic peptides can be used as ligands to form highly ordered, two-dimensional, peptide-based metal-organic coordination networks. The networks are formed on a Au(111) surface through coadsorption of cyclic dialanine with Cu-adatoms under Ultra-High Vacuum (UHV) conditions. Scanning Tunneling Microscopy (STM) in combination with X-ray Photoelectron spectroscopy (XPS) has been utilized to characterize the network structures at submolecular resolution and expound the chemical changes involved in network coordination. The networks involve a motif of three cyclic dialanine molecules coordinating to a central Cu-adatom. Interestingly the networks expose pores functionalized by the side chain of the cyclic peptide, suggesting a general method to form functionalized porous metal-organic networks on surfaces.

Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range

By monitoring ionization and fragmentation after single-photon absorption, we show that an isolated collagen triple helix model is stabilized by proline hydroxylation.

Structures of cycloserine and 2-oxazolidinone probed by X-ray photoelectron spectroscopy: theory and experiment

The electronic structures and properties of 2-oxazolidinone and the related compound cycloserine (CS) have been investigated using theoretical calculations and core and valence photoelectron spectroscopy. Isomerization of the central oxazolidine heterocycle and the addition of an amino group yield cycloserine. Theory correctly predicts the C, N, and O 1s core spectra, and additionally, we report theoretical natural bond orbital (NBO) charges. The valence ionization energies are also in agreement with theory and previous measurements. Although the lowest binding energy part of the spectra of the two compounds shows superficial similarities, further analysis of the charge densities of the frontier orbitals indicates substantial reorganization of the wave functions as a result of isomerization. The highest occupied molecular orbital (HOMO) of CS shows leading carbonyl π character with contributions from other heavy (non-H) atoms in the molecule, while the HOMO of 2-oxazolidinone (OX2) has leading nitrogen, carbon, and oxygen pπ characters. The present study further theoretically predicts bond resonance effects of the compounds, evidence for which is provided by our experimental measurements and published crystallographic data.

Cyclic dipeptide immobilization on Au(111) and Cu(110) surfaces

Soft X-ray Photoelectron Spectroscopy (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy have been used to probe the electronic and adsorption properties of two cyclic dipeptides, i.e. cyclo(glycyl-histidyl) and cyclo(phenylalanyl-prolyl), on Au(111) and Cu(110) surfaces. The core level spectra show chemical shifts which indicate weak chemisorption on Au(111), and stronger chemisorption on the Cu(110) surface, mainly via one of the nitrogen atoms in the central rings of both molecules, and nitrogen in the imidazole ring of cyclo(glycyl-histidyl). From the angular dependence of the NEXAFS spectra at the O and N K-edges, we conclude that both dipeptides have a preferred orientation on the two surfaces.

Fragment based electronic structural analysis of l-phenylalanine using calculated ionization spectroscopy and dual space analysis

Fragmentation schemes in phenylalanine revealed using ionization spectroscopy and dual space analysis.

Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly

We have investigated the electronic structure of three cyclic dipeptides: cyclo(Histidyl-Glycyl) (cHisGly), cyclo(Tyrosyl-Prolyl) (cTyrPro), and cyclo(Phenylalanyl-Phenylalanyl) (cPhePhe) in the vapor phase, by means of photoemission spectroscopy and theoretical modeling. The last compound was evaporated from the solid linear dipeptide, but cyclised, losing water to form cPhePhe in the gas phase. The results are compared with our previous studies of three other cyclopeptides. Experimental valence and core level spectra have been interpreted in the light of calculations to identify the basic chemical properties associated with the central diketopiperazine ring, and with the additional functional groups. The valence spectra are generally characterized by a restricted set of outer valence orbitals separated by a gap from most other valence orbitals. The theoretically simulated core and valence spectra of all three cyclic dipeptides agree reasonably well with the experimental spectra. The central ring and the side chains act as independent chromophores whose spectra do not influence one another, except for prolyl dipeptides, where the pyrrole ring is fused with the central ring. In this case, significant changes in the valence and core level spectra were observed, and explained by stronger hybridization of the valence orbitals.