Photoemission and the shape of amino acids

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.

PECD study of a single conformer molecule: a critical comparison of experiment and theory

In this work we address a specific experimental and theoretical quest on the influence of a conformational population in the modeling of PhotoElectron Circular Dichroism spectroscopy. In the last two...

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...

Experimental and Theoretical Soft X-ray Study of Nicotine and Related Compounds

The valence and core electronic structure of nicotine, nicotinic acid, and nicotinamide have been studied by photoelectron and soft X-ray absorption spectroscopy, supported by theoretical calculations, which take into account conformational isomerism. The core-level photoionization spectra of all molecules have been assigned, and theory indicates that the effects of conformational differences are small, generally less than the natural line widths of the core ionic states. However, in the case of nicotinamide, the theoretical valence ionization potentials of cis and trans conformers differ significantly in the outer valence space, and the experimental spectrum is in agreement with the calculated outer valence cis conformer spectrum. In addition, the C, N, and O K edge near-edge absorption fine structure spectra are reported and interpreted by comparison with reference compounds. We find evidence at the N and O K edges of interaction between the delocalized orbitals of the pyridine ring and the substituents for nicotinic acid and nicotinamide. The strength of the interaction varies because the first is planar, while the second is twisted, reducing the extent of orbital mixing.

Predicting Core Level Photoelectron Spectra of Amino Acids Using Density Functional Theory

Core level photoelectron spectroscopy is a widely used technique to study amino acids. Interpretation of the individual contributions from functional groups and their local chemical environments to overall spectra requires both high-resolution reference spectra and theoretical insights, for example, from density functional theory calculations. This is a particular challenge for crystalline amino acids due to the lack of experimental data and the limitation of previous calculations to gas phase molecules. Here, a state of the art multiresolution approach is used for high-precision gas phase calculations and to validate core hole pseudopotentials for plane-wave calculations. This powerful combination of complementary numerical techniques provides a framework for accurate ΔSCF calculations for molecules and solids in systematic basis sets. It is used to successfully predict C and O 1s core level spectra of glycine, alanine, and serine and identify chemical state contributions to experimental spectra of crystalline amino acids.

An experimental and theoretical investigation of XPS and NEXAFS of 5-halouracils

The C, N and O 1s excitation and ionization processes of 5X-uracil (X = F, Cl, Br, and I) were investigated using near edge X-ray absorption fine structure (NEXAFS) and X-ray photoemission (XPS) spectroscopies. This study aims at the fine assessment of the effects of the functionalization of uracil molecules by halogen atoms having different electronegativity and bound to the same molecular site. Two DFT-based approaches, which rely on different paradigms, have been used to simulate the experimental spectra and to assign the corresponding features. The analysis of the screening of the core holes of the different atoms via electronic charge density plots has turned out to be a useful tool to illustrate the competition between the partially aromatic and partially conjugate properties of this class of molecules.

Identification of the smallest peptide with a zwitterion as the global minimum: a first-principles study on arginine-containing peptides

Zwitterions are believed to play an important role in determining the structures, properties and functions of peptides and proteins. However, the smallest peptide with a zwitterionic structure as the global minimum in the gas phase is still not yet identified. In this study, an effective step-by-step strategy has been used to characterize the stable conformers of arginine-containing peptides arginylalanine (ArgAla) and arginylserine (ArgSer). Energy calculations at the DSD-PBEP86-D3BJ/aug-cc-pVTZ level and further extrapolation to the complete basis set (CBS) limit have confirmed, for the first time, that ArgSer appears to be a promising candidate as the smallest peptide with a zwitterionic global minimum structure. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of these arginine-containing peptides. Notable spectral differences were found which enable the unambiguous identification of different neutral forms in future experiments. Our study thus provides valuable insights into the structural stability of zwitterions with the increase of molecular size and illustrates the competition between the canonical and zwitterionic isomers.

Experimental and theoretical XPS and NEXAFS studies of N-methylacetamide and N-methyltrifluoroacetamide

Experimental and theoretical spectra of N-methylacetamide and N-methyltrifluoroacetamide at the K-edges are reported.

Functionalization of nanostructured cerium oxide films with histidine

The surfaces of polycrystalline cerium oxide films were modified by histidine adsorption under vacuum and characterized by the synchrotron based techniques of core and valence level photoemission, resonant photoemission and near edge X-ray absorption spectroscopy, as well as atomic force microscopy. Histidine is strongly bound to the oxide surface in the anionic form through the deprotonated carboxylate group, and forms a disordered molecular adlayer. The imidazole ring and the amino side group do not form bonds with the substrate but are involved in the intermolecular hydrogen bonding which stabilizes the molecular adlayer. The surface reaction with histidine results in water desorption accompanied by oxide reduction, which is propagated into the bulk of the film. Previously studied, well-characterized surfaces are a guide to the chemistry of the present polycrystalline surface and histidine bonds via the carboxylate group in both cases. In contrast, bonding via the imidazole group occurs on the well-ordered surface but not in the present case. The morphology and structure of the cerium oxide are decisive factors which define the adsorption geometry of the histidine adlayer.

Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

The global minimum of the dipeptide ArgGly is found to be in the canonical form, rather than the zwitterionic form.

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.

Franck–Condon factors—Computational approaches and recent developments

Algorithms and methodologies for the calculation of Franck–Condon integrals are reviewed. Starting from the standard approach based on the Cartesian representation of the normal modes and the use of Duschinsky's transformation and recursion formulas, methods for treating large displacements of the equilibrium positions and anharmonic and non-Condon effects are considered. Finally, focusing attention on problems arising from the use of recurrence relations, some of the proposed solutions are critically reviewed along with new alternative approaches.

Valence structures of aromatic bioactive compounds: a combined theoretical and experimental study

Valence electronic structures of three recently isolated aryl bioactive compounds, namely 2-phenylethanol (2PE), p-hydroxyphenylethanol (HPE) and 4-hydroxybenzaldehyde (HBA), are studied using a combined theoretical and experimental method. Density functional theory-based calculations indicate that the side chains cause electron charge redistribution and therefore influence the aromaticity of the benzene derivatives. The simulated IR spectra further reveal features induced by the side chains. Solvent effects on the IR spectra are simulated using the polarizable continuum model, which exhibits enhancement of the O-H stretch vibrations with significant red-shift of 464 cm(-1) in 2PE. A significant spectral peak splitting of 94 cm(-1) between O(4)-H and O(8)-H of HPE is revealed in an aqueous environment. Experimental measurements for valence binding energy spectra for 2PE, HPE and HBA are presented and analyzed using outer-valence Green function calculations. The experimental (predicted) first ionization energies are measured as 9.19 (8.79), 8.47 (8.27) and 8.97 (8.82) eV for 2PE, HPE and HBA, respectively. The frontier orbitals (highest occupied molecular orbitals, HOMOs, and lowest unoccupied molecular orbitals, LUMOs) have similar atomic orbital characters although the HOMO-LUMO energy gaps are quite different.

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.

Calculated vertical ionization energies of the common α-amino acids in the gas phase and in solution

The vertical ionization energies of the low-lying conformers of the α-amino acids found in proteins have been calculated. Geometry optimizations were first performed at the B3LYP/6-311G(d,p) level of theory, and then reoptimized at the MP2/6-311G(d,p) level of theory. Vertical ionization energies were then computed by three methods, electron propagator in the partial third-order (P3) approximation, Outer-Valence-Green's Functions, and by evaluating the difference in the total energy between the cation radical and the neutral amino acid in the geometry of the neutral species. When available, the results are compared to the experimental vertical ionization energies. The vertical ionization energies calculated using the MP2/P3 method gave the best overall agreement with the experimental results. Next, the ionization energies in solution are calculated for the zwitterionic forms of the α-amino acids by using IEFPCM methods. To obtain the vertical ionization energy in solution, it is necessary to use the nonequilibrium polarizable continuum model (NEPCM), the results of which are reported here for the α-amino acids.

On the origins of core-electron chemical shifts of small biomolecules in aqueous solution: insights from photoemission and ab initio calculations of glycine(aq)

The local electronic structure of glycine in neutral, basic, and acidic aqueous solution is studied experimentally by X-ray photoelectron spectroscopy and theoretically by molecular dynamics simulations accompanied by first-principle electronic structure and spectrum calculations. Measured and computed nitrogen and carbon 1s binding energies are assigned to different local atomic environments, which are shown to be sensitive to the protonation/deprotonation of the amino and carboxyl functional groups at different pH values. We report the first accurate computation of core-level chemical shifts of an aqueous solute in various protonation states and explicitly show how the distributions of photoelectron binding energies (core-level peak widths) are related to the details of the hydrogen bond configurations, i.e. the geometries of the water solvation shell and the associated electronic screening. The comparison between the experiments and calculations further enables the separation of protonation-induced (covalent) and solvent-induced (electrostatic) screening contributions to the chemical shifts in the aqueous phase. The present core-level line shape analysis facilitates an accurate interpretation of photoelectron spectra from larger biomolecular solutes than glycine.

Pyrimidine and halogenated pyrimidines near edge x-ray absorption fine structure spectra at C and N K-edges: experiment and theory

The inner shell excitation of pyrimidine and some halogenated pyrimidines near the C and N K-edges has been investigated experimentally by near edge x-ray absorption fine structure spectroscopy and theoretically by density functional theory calculations. The selected targets, 5-Br-pyrimidine, 2-Br-pyrimidine, 2-Cl-pyrimidine, and 5-Br-2-Cl-pyrimidine, allow the effects of the functionalization of the pyrimidine ring to be studied either as a function of different halogen atoms bound to the same molecular site or as a function of the same halogen atom bound to different molecular sites. The results show that the individual characteristics of the different spectra of the substituted pyrimidines can be rationalized in terms of variations in electronic and geometrical structures of the molecule depending on the localization and the electronegativity of the substituent.

Investigation of halogenated pyrimidines by X-ray photoemission spectroscopy and theoretical DFT methods

The inner shell ionization of pyrimidine and some halogenated pyrimidines has been investigated experimentally by X-ray photoemission spectroscopy (XPS) and theoretically by density functional theory (DFT) methods. The selected targets-5-Br-pyrimidine, 2-Br-pyrimidine, 2-Cl-pyrimidine, and 5-Br-2-Cl-pyrimidine-allowed the study of the effect of the functionalization of the pyrimidine ring by different halogen atoms bound to the same molecular site, or by the same halogen atom bound to different molecular sites. The theoretical investigation of the inductive and resonance effects in the C(1s) ionization confirms the soundness of the resonance model for a qualitative description of the properties of an aromatic system. Moreover, the combination of the experimental results and the theoretical analysis provides a detailed description of the effects of the halogen atom on the screening of a C(1s) hole in the aromatic pyrimidine ring.

Peptide/TiO2 surface interaction: a theoretical and experimental study on the structure of adsorbed ALA-GLU and ALA-LYS

The adsorption on the TiO(2) surface of two dipeptides AE (L-alanine-L-glutamic acid) and AK (L-alanine-L-lysine), that are "building blocks" of the more complex oligopeptide EAK16, has been investigated both theoretically and experimentally. Classical molecular dynamics simulations have been used to study the adsorption of H-Ala-Glu-NH(2) and H-Ala-Lys-NH(2) dipeptides onto a rutile TiO(2) (110) surface in water solution. Several peptide conformers have been considered simultaneously upon the surface. The most probable contact points between the molecules and the surface have been identified. Carbonyl oxygens as well as nitrogen atoms are possible Ti coordination points. Local effects are responsible for adsorption and desorption events. Self-interaction effects can induce molecular reorientations giving less strongly adsorbed species. The chemical structure and composition of thin films of the two dipeptides AE and AK on TiO(2) were investigated by XPS (X-ray photoelectron spectroscopy) measurements at both O and N K-edges. Theoretical ab initio calculations (DeltaSCF) were also performed to simulate the spectra, allowing for a direct comparison between experiment and theory.