Investigation of the Gas-Phase Amino Acid Alanine by Synchrotron Radiation Photoelectron Spectroscopy

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.

Wavefunction-based quantum-chemicalab initiocalculations for core electron binding energies of small open shell molecules

Core electron binding energies (CEBEs), i.e. ionization energies of 1s core orbitals, are calculated by means of wavefunction-based quantum-chemicalab initiomethods for a series of small open-shell molecules containing first-row atoms. The calculations are performed in three steps: (a) Koopmans' theorem, where the orbitals of the electronic ground state are used unchanged also for the ions, (b) Hartree-Fock or self consistent field (SCF) approximation in which the orbitals are allowed to relax after 1s ionization (ΔSCF), (c) dynamic correlation effects on top of SCF. For open-shell molecules 1s ionization leads to ions in several spin states, mostly to a pair of a triplet and a singlet state. In several cases one or both of these ionic states are only poorly described by a single-reference SCF wavefunction, therefore a multi-reference complete active space self consistent field (CAS-SCF) wavefunction is used instead. The correlation effects are evaluated by means of our multi-reference coupled electron pair approximation program. The accuracy of the calculated CEBEs is in the order of 0.1-0.4 eV. This is in agreement with experimental results for NO and O₂. But there exist only very few gas phase data for CEBEs of open-shell molecules.

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...

Hydrocarboxyl Radical as a Product of α-Alanine Ultraviolet Photolysis

UV photodissociation of α-alanine was studied by parahydrogen matrix isolation infrared spectroscopy. The temporal behavior of Fourier transform infrared spectra revealed that UV irradiation at 213 nm yielded the HOCO radical as a direct photoproduct from the S₂ excited state. The concentration of HOCO quickly approached a steady state due to secondary photodissociation of HOCO to produce CO₂ + H or CO + OH. On the other hand, no photoproducts were detected by S₁ excitation at 266 nm. Irradiation of fully deuterated α-alanine at 213 nm yielded ∼2 times more cis-DOCO radicals than the lower energy isomer trans-DOCO, indicating that the conformation of the hydroxyl group is fairly well-preserved upon photodissociation of α-alanine. The present study suggests that HOCO may be a good tracer species in the search for amino acids in interstellar space.

A Comprehensive Picture of the Structures, Energies, and Bonding in the Alanine Dimers

High level quantum mechanical computations and extensive stochastic searches of the potential energy surfaces of the Alanine dimers uncover rich and complex structural and interaction landscapes. A total of 416 strongly bound (up 13.4 kcal mol^-1 binding energies at the DLPNO-CCSD(T)/6-311++G(d,p) level corrected by the basis set superposition error and by the zero point vibrational energies over B3LYP-D3 geometries), close energy equilibrium structures were located, bonded via 32 specific types of intermolecular contacts including Y⋅⋅⋅H-X primary and Y⋅⋅⋅H-C secondary hydrogen bonds, H⋅⋅⋅H dihydrogen contacts, and non conventional anti-electrostatic Y δ - ⋯ X δ - interactions. The putative global minimum is triply degenerate, corresponding to the structure of the common dimer of a carboxylic acid. All quantum descriptors of chemical bonding point to a multitude of weak individual interactions within each dimer, whose cumulative effect results in large binding energies and in an attractive fluxional wall of non-covalent interactions in the interstitial region between the monomers.

Local electronic structure of histidine in aqueous solution

X-Ray spectroscopy coupled with DFT calculations reveals the pH dependent electronic structure of an amino acid in an aqueous environment.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

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.

Photochemical Chiral Symmetry Breaking in Alanine

We introduce a general theoretical approach for the simulation of photochemical dynamics under the influence of circularly polarized light to explore the possibility of generating enantiomeric enrichment through polarized-light-selective photochemistry. The method is applied to the simulation of the photolysis of alanine, a prototype chiral amino acid. We show that a systematic enantiomeric enrichment can be obtained depending on the helicity of the circularly polarized light that induces the excited-state photochemistry of alanine. By analyzing the patterns of the photoinduced fragmentation of alanine we find an inducible enantiomeric enrichment up to 1.7%, which is also in good correspondence to the experimental findings. Our method is generally applicable to complex systems and might serve to systematically explore the photochemical origin of homochirality.

Isolated neutral peptides

This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.

A source for microhydrated biomolecules

We describe the construction of an apparatus for the production of a molecular jet of microhydrated biomolecules. Our design uses a water reservoir producing water vapour, which then passes through a separate reservoir containing a vapour of a sublimated biomolecule. The mixture coexpands into a molecular beam apparatus through a conical nozzle. Mass spectra showing water-adenin and water-uracil complexes are shown as typical examples. Suitable expansion conditions are reached without the use of an inert carrier gas.

VUV photodynamics and chiral asymmetry in the photoionization of gas phase alanine enantiomers

The valence shell photoionization of the simplest proteinaceous chiral amino acid, alanine, is investigated over the vacuum ultraviolet region from its ionization threshold up to 18 eV. Tunable and variable polarization synchrotron radiation was coupled to a double imaging photoelectron/photoion coincidence (i(2)PEPICO) spectrometer to produce mass-selected threshold photoelectron spectra and derive the state-selected fragmentation channels. The photoelectron circular dichroism (PECD), an orbital-sensitive, conformer-dependent chiroptical effect, was also recorded at various photon energies and compared to continuum multiple scattering calculations. Two complementary vaporization methods-aerosol thermodesorption and a resistively heated sample oven coupled to an adiabatic expansion-were applied to promote pure enantiomers of alanine into the gas phase, yielding neutral alanine with different internal energy distributions. A comparison of the photoelectron spectroscopy, fragmentation, and dichroism measured for each of the vaporization methods was rationalized in terms of internal energy and conformer populations and supported by theoretical calculations. The analytical potential of the so-called PECD-PICO detection technique-where the electron spectroscopy and circular dichroism can be obtained as a function of mass and ion translational energy-is underlined and applied to characterize the origin of the various species found in the experimental mass spectra. Finally, the PECD findings are discussed within an astrochemical context, and possible implications regarding the origin of biomolecular asymmetry are identified.

Effects of alkyl side chains on properties of aliphatic amino acids probed using quantum chemical calculations

Effects of alkyl side chains (R-) on the electronic structural properties of aliphatic amino acids are investigated using quantum mechanical approaches. The carbon (C 1s) binding energy spectra of the aliphatic amino acids are derived from the C 1s spectrum of glycine (the parent spectrum) by the addition of spectral peaks, depending on the alkyl side chains, appearing in the lower energy region IP < 290 eV (where IP is the ionization potential). The two glycyl parent spectral peaks of the amide 291.0 eV [C((2))] and carboxylic 293.5 eV [C((1))] C atoms are shifted in the aliphatic amino acids owing to perturbations depending on the size and structure of the alkyl chains. The pattern of the N 1s and O 1s spectra in glycine is retained in the spectra of the other amino acids with small shifts to lower energy, again depending on the alkyl side chain. The Hirshfeld charge analyses confirm the observations. The alkyl effects on the valence binding energy spectra of the amino acids are concentrated in the middle valence energy region of 12-16 eV, and hence this energy region of 12-16 eV is considered as the `fingerprint' of the alkyl side chains. Selected valence orbitals, either inside or outside of the alkyl fingerprint region, are presented using both density distributions and orbital momentum distributions, in order to understand the chemical bonding of the amino acids. It is also observed that the HOMO-LUMO energy gaps of the aliphatic amino acids are reduced with the growth of the alkyl side chain.

Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1-(β-D-ribofuranosyl)-2-pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1-(β-D-ribofuranosyl)-5-methyl-2-pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital-based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine.

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.

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.

Vibrational and electronic characterisation of Staphylococcus aureus wall teichoic acids and relevant components in thin films

This work reports an investigation of S. aureus wall teichoic acid (WTA) and compares this biopolymer with its major occurring components, D: -alanine and glycerol phosphate. Detailed insight into molecular structures and electronic properties is obtained by vibrational and photoemission spectroscopy. Calculations are performed to support the analysis of our experimental vibrational spectra. It is shown that there are contributions of positive and negative charges in WTAs, but the number of negative charges is expected to be higher. The presence of both positive and negative charges on WTA may offer a route for modification of surfaces with the objective of avoiding the formation of biofilms.

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.

A reevaluation of computed proton affinities for the common alpha-amino acids

The proton affinities of the 20 common amino acids have been computed at the G3MP2 level using structures derived from broad conformational searches at a variety of levels including G3MP2. In some cases, the conformational surveys identified more stable species than had been used in previous studies of proton affinities, though the differences in energy are sometimes rather small. The present values are likely the most reliable measure of amino acid proton affinities in the gas phase. An analysis of differences between these values and those obtained experimentally via the kinetic method indicates that the extraction of proton affinities from kinetic method data can potentially lead to large errors linked to the estimation of relative protonation entropies.

Reactivity and core-ionization energies in conjugated dienes. Carbon 1s photoelectron spectroscopy of 1,3-pentadiene

The high-resolution carbon 1s photoelectron spectrum of trans-1,3-pentadiene has been resolved into contributions from the five inequivalent carbon atoms, and carbon 1s ionization energies have been assigned to each of these atoms. Spectra have also been measured for propene and 1,3-butadiene at better resolution than has previously been available. The ionization energies for the sp2 carbons are found to correlate well with activation energies for electrophilic addition and with proton affinities. Comparing the results for 1,3-pentadiene with those for ethene, propene, and 1,3-butadiene as well as with results of theoretical calculations makes it is possible to assess the effect of the terminal methyl group in 1,3-pentadiene. As in propene, the methyl group contributes electrons to the beta carbon through the pi system. In addition, there is a significant (though smaller) contribution from the methyl group to the terminal (delta) CH2 carbon, also through the pi system. Most of the effect of the methyl group is present in the ground-state molecule. There are only relatively small contributions from the methyl group to the ionization energies from redistribution of charge in the pi system in response to the removal of a core electron. In addition to these specific effects, there is an overall decrease in average ionization energy as the size of the molecule increases as well as effects that are specific to the conjugated systems in 1,3-butadiene and 1,3-pentadiene. The results provide insight into the reactivity and regioselectivity of conjugated dienes.

Electronic excitations of glycine, alanine, and cysteine conformers from first-principles calculations

The electronic and optical properties are studied for three conformers of amino acid molecules using gradient-corrected (spin-) density functional theory within a projector-augmented wave scheme and the supercell method. We investigate single-particle excitations such as ionization energies and electron affinities as well as pair excitations. By comparing eigenvalues resulting from several local and nonlocal energy functionals, the influence of treatment of exchange and correlation is demonstrated. The excitations are described within the Delta-self-consistent field method with an occupation number constraint to obtain excitation energies and Stokes shifts. The results are used to also discuss the optical absorption properties. In contrast to the lowest single- and two-particle excitation energies, remarkable changes are found in absorption spectra in dependence on the conformation of the molecule geometry.

Nitrogen 1s Near-Edge X-ray Absorption Fine Structure Spectroscopy of Amino Acids: Resolving Zwitterionic Effects

Considerable variation is observed in the near-edge X-ray absorption fine structure (NEXAFS) spectra of amino acids. To unambiguously characterize the chemical origin of this variation, we have acquired the nitrogen 1s NEXAFS spectra of several amino acids and other model compounds and complemented these experimental measurements with ab initio calculations of isolated molecules and molecular clusters. The systematic differences observed between the zwitterionic and un-ionized forms of amino acids arise directly from the structural difference (-NH2 vs -NH3+), which leads to a change in the degree of Rydberg-valence mixing. Further change arises from quenching of this Rydberg character in the spectra of condensed amino acids. Ab initio calculations are used to explore the degree of Rydberg-valence mixing in the solid state.

Conformation Effects on the Electronic Structures of β-Alanine

Ten low-lying conformers of beta-alanine have been studied by the hybrid density functional B3LYP/aug-cc-pVDZ method. Energetic extrapolation calculations at the MP3 and MP4(SDQ) levels of theory and the theoretical photoelectron spectra simulated with the electron propagation theory demonstrate that there are at least three gauche conformers (G1, G2, and G3) in gas-phase experiments. The calculated ionization potentials are in good agreement with the experimental data available in the literature. Natural bond orbital and atoms-in-molecules analyses exhibit a remarkable influence on the molecular electronic structures by the strong intramolecular hydrogen bonding O-H...N in the neutral conformer G2. Remarkable internal rotations of the COOH group are found in the cationic G1+ and G3+ with respect to the neutral conformers. A distonic [NH3+-(CH2)2-COO*] radical can be formed through the spontaneous intramolecular proton transfer in G2+. A novel intramolecular hydrogen bonding, C-H...O, is found in the anti A1+ cation.