Glycine Valence Orbital Electron Densities: Comparison of Electron Momentum Spectroscopy Experiments with Hartree−Fock and Density Functional Theories

Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy

In the present contribution, we use x-rays to monitor charge-induced chemical dynamics in the photoionized amino acid glycine with femtosecond time resolution. The outgoing photoelectron leaves behind the cation in a coherent superposition of quantum mechanical eigenstates. Delayed x-ray pulses track the induced coherence through resonant x-ray absorption that induces Auger decay. Temporal modulation of the Auger electron signal correlated with specific ions is observed, which is governed by the initial electronic coherence and subsequent vibronic coupling to nuclear degrees of freedom. In the time-resolved x-ray absorption measurement, we monitor the time-frequency spectra of the resulting many-body quantum wave packets for a period of 175 fs along different reaction coordinates. Our experiment proves that by measuring specific fragments associated with the glycine dication as a function of the pump-probe delay, one can selectively probe electronic coherences at early times associated with a few distinguishable components of the broad electronic wave packet created initially by the pump pulse in the cation. The corresponding coherent superpositions formed by subsets of electronic eigenstates and evolving along parallel dynamical pathways show different phases and time periods in the range of ( - 0.3 ± 0.1 ) π ≤ ϕ ≤ ( 0.1 ± 0.2 ) π and 18.2 - 1.4 + 1.7 ≤ T ≤ 23.9 - 1.1 + 1.2 fs. Furthermore, for long delays, the data allow us to pinpoint the driving vibrational modes of chemical dynamics mediating charge-induced bond cleavage along different reaction coordinates.

A high level theory investigation on the lowest-lying ionization potentials of glycine (NH2CH2COOH)

In this work, an investigation on the ionization potentials (IPs) of the glycine molecule (NH₂CH₂COOH) is presented. IPs ranging up to ∼20 eV were probed for each of the six conformations considered, with the referred threshold being chosen based on both: (i) the observations by recent photoelectron-photoion coincidence (PEPICO) experiments and (ii) the energy range of relevance to the modeling of other photo-induced processes (e.g., photoionization). For computing the IPs, the equation-of-motion ionization potential coupled-cluster with single and double excitations method (EOMIP-CCSD) was employed with large correlation consistent aug-cc-pVXZ and aug-cc-pCVXZ (X = D, T, and Q) basis sets. Extrapolation to the complete basis set limit and consideration of core electron correlation effects were also taken into account. Subsequently, the Feller-Peterson-Dixon (FPD) approach was used for considering all the contributions and to obtain accurate IPs. In addition, coupled-cluster with single and double excitations as well as perturbative triples, CCSD(T), was also used with the aug-cc-pVTZ basis set. When compared to each other, results obtained through the use of these approaches yielded excellent agreement. In general, the outcomes from the present work provide additional information to the insights gathered from the recent PEPICO experiments as well as accurate IPs for all 6 conformations of glycine using an approach based on high levels of theory. Hence, it is expected that other investigations focusing on photo-induced processes originating from NH₂CH₂COOH (for instance, the computational modeling of its photoionization) will be motivated for study in the future.

Electronic quantum coherence in glycine molecules probed with ultrashort x-ray pulses in real time

Here, we use x-rays to create and probe quantum coherence in the photoionized amino acid glycine. The outgoing photoelectron leaves behind the cation in a coherent superposition of quantum mechanical eigenstates. Delayed x-ray pulses track the induced coherence through resonant x-ray absorption that induces Auger decay and by photoelectron emission from sequential double photoionization. Sinusoidal temporal modulation of the detected signal at early times (0 to 25 fs) is observed in both measurements. Advanced ab initio many-electron simulations allow us to explain the first 25 fs of the detected coherent quantum evolution in terms of the electronic coherence. In the kinematically complete x-ray absorption measurement, we monitor its dynamics for a period of 175 fs and observe an evolving modulation that may implicate the coupling of electronic to vibronic coherence at longer time scales. Our experiment provides a direct support for the existence of long-lived electronic coherence in photoionized biomolecules.

Ultrafast charge dynamics in glycine induced by attosecond pulses

The combination of attosecond pump-probe techniques with mass spectrometry methods has recently led to the first experimental demonstration of ultrafast charge dynamics in a biomolecule, the amino acid phenylalanine [Calegari et al., Science, 2014, 346, 336]. Using an extension of the static-exchange density functional theory (DFT) method, the observed dynamics was explained as resulting from the coherent superposition of ionic states produced by the broadband attosecond pulse. Here, we have used the static-exchange DFT method to investigate charge migration induced by attosecond pulses in the glycine molecule. We show that the observed dynamics follows patterns similar to those previously found in phenylalanine, namely that charge fluctuations occur all over the molecule and that they can be explained in terms of a few typical frequencies of the system. We have checked the validity of our approach by explicitly comparing with the photoelectron spectra obtained in synchrotron radiation experiments and with the charge dynamics that follows the removal of an electron from a given molecular orbital, for which fully correlated ab initio results are available in the literature. From this comparison, we conclude that our method provides an accurate description of both the coherent superposition of cationic states generated by the attosecond pulse and its subsequent time evolution. Hence, we expect that the static-exchange DFT method should perform equally well for other medium-size and large molecules, for which the use of fully correlated ab initio methods is not possible.

Insights into the dissociative ionization of glycine by PEPICO experiments

The fragmentation of glycine (NH₂CH₂COOH) has been studied by photoelectron–photoion coincidence, PEPICO, experiments at 60 eV photon energy.

An investigation of hybridization and the orbital models of molecular electronic structure for CH4, NH3, and H2O

Observations of the physical behaviour (motions) of the valence (frontier) electrons in the iconic benchmark hydride molecules CH4, NH3, and H2O are used to provide a direct experimental evaluation of hybridization and of the localized and delocalized orbital models of molecular electronic structure, after more than 80 years since the initial proposals of these theoretical concepts. Our previously published experimental measurements of valence (frontier) electron momentum probability distributions, made by electron momentum spectroscopy (EMS), are compared with those calculated using the localized molecular orbital (LMO) model and a range of hybrid orbital models, as well as with the delocalized canonical molecular orbital (CMO) and density functional theory Kohn–Sham orbital (KSO) models. In all cases, the electron momentum probability distributions calculated with LMOs and localized hybrid orbital type models are inconsistent with the experimental observations. In contrast, those calculated with the delocalized CMOs and KSOs are in very good agreement with the experimental measurements. These findings are of importance in those research applications such as reactivity, drug and novel material design, and also in molecular electronics, where the shapes and orientations of particular valence (frontier) orbital electron density probability distributions (and not the total electron densities) are considered to be key determining factors. These findings and their implications are also of pedagogical significance in chemistry and molecular physics.

Soft x-ray ionization induced fragmentation of glycine

X-ray absorption commonly involves dissociative core ionization producing not only momentum correlated charged fragments but also low- and high-energy electrons capable of inducing damage in living tissue. This gives a natural motivation for studying the core ionization induced fragmentation processes in biologically important molecules such as amino acids. Here the fragmentation of amino acid glycine following carbon 1s core ionization has been studied. Using photoelectron-photoion-photoion coincidence technique, a detailed analysis on fragmentation of the sample molecule into pairs of momentum correlated cations has been carried out. The main characteristics of core ionization induced fragmentation of glycine were found to be the rupture of the C-Cα bond and the presence of the CNH(2)(+) fragment.

Analysis of a measurement scheme for ultrafast hole dynamics by few femtosecond resolution X-ray pump–probe Auger spectroscopy

Ultrafast hole dynamics created in molecular systems as a result of sudden ionisation is the focus of much attention in the field of attosecond science. Using the molecule glycine we show through ab initio simulations that the dynamics of a hole, arising from ionisation in the inner valence region, evolves with a timescale appropriate to be measured using X-ray pulses from the current generation of SASE free electron lasers. The examined pump–probe scheme uses X-rays with photon energy below the K edge of carbon (275–280 eV) that will ionise from the inner valence region. A second probe X-ray at the same energy can excite an electron from the core to fill the vacancy in the inner-valence region. The dynamics of the inner valence hole can be tracked by measuring the Auger electrons produced by the subsequent refilling of the core hole as a function of pump–probe delay. We consider the feasibility of the experiment and include numerical simulation to support this analysis. We discuss the potential for all X-ray pump-X-ray probe Auger spectroscopy measurements for tracking hole migration.

Imaging Momentum Orbital Densities of Conformationally Versatile Molecules: A Benchmark Theoretical Study of the Molecular and Electronic Structures of Dimethoxymethane

The main purpose of the present work is to predict from benchmark many-body quantum mechanical calculations the results of experimental studies of the valence electronic structure of dimethoxymethane employing electron momentum spectroscopy, and to establish once and for all the guidelines that should systematically be followed in order to reliably interpret the results of such experiments on conformationally versatile molecules. In a first step, accurate calculations of the energy differences between stationary points on the potential energy surface of this molecule are performed using Hartree-Fock (HF) theory and post-HF treatments of improving quality (MP2, MP3, CCSD, CCSD(T), along with basis sets of increasing size. This study focuses on the four conformers of this molecule, namely the trans-trans (TT), trans-gauche (TG), gauche-gauche (G+G+), and gauche-gauche (G+G-) structures, belonging to the C2v, C1, C2, and Cs symmetry point groups, respectively. A focal point analysis supplemented by suited extrapolations to the limit of asymptotically complete basis sets is carried out to determine how the conformational energy differences at 0 K approach the full CI limit. In a second step, statistical thermodynamics accounting for hindered rotations is used to calculate Gibbs free energy corrections to the above energy differences, and to evaluate the abundance of each conformer in the gas phase. It is found that, at room temperature, the G+G+ species accounts for 96% of the conformational mixture characterizing dimethoxymethane. In a third step, the valence one-electron and shake-up ionization spectrum of dimethoxymethane is analyzed according to calculations on the G+G+ conformer alone by means of one-particle Green's function [1p-GF] theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. A complete breakdown of the orbital picture of ionization is noted at electron binding energies above 22 eV. A comparison with available (e,2e) ionization spectra enables us to identify specific fingerprints of through-space orbital interactions associated with the anomeric effect. At last, based on our 1p-GF/ADC(3) assignment of spectral bands, accurate and spherically averaged (e,2e) electron momentum distributions at an electron impact energy of 1200 eV are computed from the related Dyson orbitals. Very significant discrepancies are observed with momentum distributions obtained for several outer-valence levels using standard Kohn-Sham orbitals.

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.

Study of the molecular structure, ionization spectrum, and electronic wave function of 1,3-butadiene using electron momentum spectroscopy and benchmark Dyson orbital theories

The scope of the present work is to reconcile electron momentum spectroscopy with elementary thermodynamics, and refute conclusions drawn by Saha et al. in J. Chem. Phys. 123, 124315 (2005) regarding fingerprints of the gauche conformational isomer of 1,3-butadiene in electron momentum distributions that were experimentally inferred from gas phase (e,2e) measurements on this compound [M. J. Brunger et al., J. Chem. Phys. 108, 1859 (1998)]. Our analysis is based on thorough calculations of one-electron and shake-up ionization spectra employing one-particle Green's function theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. Accurate spherically averaged electron momentum distributions are correspondingly computed from the related Dyson orbitals. The ionization spectra and Dyson orbital momentum distributions that were computed for the trans-conformer of 1,3-butadiene alone are amply sufficient to quantitatively unravel the shape of all available experimental (e,2e) electron momentum distributions. A comparison of theoretical ADC(3) spectra for the s-trans and gauche energy minima with inner- and outer-valence high-resolution photoelectron measurements employing a synchrotron radiation beam [D. M. P. Holland et al., J. Phys. B 29, 3091 (1996)] demonstrates that the gauche structure is incompatible with ionization experiments in high-vacuum conditions and at standard temperatures. On the other hand, outer-valence Green's function calculations on the s-trans energy minimum form and approaching basis set completeness provide highly quantitative insights, within approximately 0.2 eV accuracy, into the available experimental one-electron ionization energies. At last, analysis of the angular dependence of relative (e,2e) ionization intensities nicely confirms the presence of one rather intense pi(-2) pi(*+1) satellite at approximately 13.1 eV in the ionization spectrum of the s-trans conformer.

Orbital based electronic structural signatures of the guanine keto G-7H/G-9H tautomer pair as studied using dual space analysis

Electronic structural signatures of the guanine-7H and guanine-9H tautomers have been investigated on an orbital by orbital basis using dual space analysis. A combination of density functional theory (B3LYP/TZVP), the statistical average of model orbital potentials (SAOP/TZ2P) method and outer valence Green's function theory (OVGF/TZVP) has been used to generate optimal tautomer geometries and accurate ionization energy spectra for the guanine tautomer pair. The present work found that the non-planar form for both of the guanine keto pair possesses lower energies than their corresponding planar counterparts, and that the canonical form of the guanine-7H tautomer has slightly lower total energy than guanine-9H. This latter result is in agreement with previous experimental and theoretical findings. In the planar guanine pair the geometric parameters and anisotropic molecular properties are compared, focusing on changes caused by the mobile proton transfer. It is demonstrated that the mobile proton only causes limited disturbance to isotropic properties, such as geometry and the energetics, of the guanine keto tautomer pair. The exception to this general statement is for related local changes such as the N((7))-C((8)) and C((8))-N((9)) bond length resonance between the single and double bonds, reflecting the nitrogen atom being bonded with the mobile proton in the tautomers. The mobile proton distorts the electron distribution of the tautomers, which leads to significant changes in the molecular anisotropic properties. The dipole moment of guanine-7H is altered by about a factor of three, from 2.23 to 7.05 D (guanine-9H), and the molecular electrostatic potentials also reflect significant electron charge distortion. The outer valence orbital momentum distributions, which were obtained using the plane wave impulse approximation (PWIA), have demonstrated quantitatively that the outer valence orbitals of the tautomer pair can be divided into three groups. That is orbitals 1a''-7a'' and 18a', which do not have visible alternations in the tautomeric process (which consist of either pi orbitals or are close to the inner valence shell); a second group comprising orbitals 19a'-22a', 25a', 26a', 28a', 29a' and 31a', which show small perturbations as a result of the mobile hydrogen locations; and group three, orbitals 23a', 24a', 27a', 30a' and 32a', which demonstrate significant changes due to the mobile proton transfer and are therefore considered as signature orbitals of the G-7H/G-9H keto tautomeric process.

Understanding glycine conformation through molecular orbitals

The four most stable C(s) conformers of glycine have been investigated using a variety of quantum-mechanical methods based on Hartree-Fock theory, density-functional theory (B3LYP and statistical average of orbital potential), and electron propagation (OVGF) treatments. Information obtained from these models were analyzed in coordinate and momentum spaces using dual space analysis to provide insight based on orbitals into the bonding mechanisms of glycine conformers, which are generated by rotation of C-O(H) (II), C-C (III), and C-N (IV) bonds from the global minimum structure (I). Wave functions generated from the B3LYP/TZVP model revealed that each rotation produced a unique set of fingerprint orbitals that correspond to a specific group of outer valence orbitals, generally of a' symmetry. Orbitals 14a', 13a', 12a', and 11a' are identified as the fingerprint orbitals for the C-O(H) (II) rotation, whereas fingerprint orbitals for the C-C (III) bond rotation are located as 16a' [highest occupied molecular orbital (HOMO)], 15a' [next highest molecular occupied molecular orbital (NHOMO)], 14a', and 12a' orbitals. Fingerprint orbitals for IV generated by the combined rotations around the C-C, C-O(H), and C-N bonds are found as 16a', 15a', 14a', 13a', and 11a', as well as in orbitals 2a" and 1a". Orbital 14a' is identified as the fingerprint orbital for all three conformational processes, as it is the only orbital in the outer valence region which is significantly affected by the conformational processes regardless rotation of which bond. Binding energies, molecular geometries, and other molecular properties such as dipole moments calculated based on the specified treatments agree well with available experimental measurements and with previous theoretical calculation.

Probing molecular conformations with electron momentum spectroscopy: the case of n-butane

High-resolution (e,2e) measurements of the valence electronic structure and momentum-space electron density distributions of n-butane have been exhaustively reanalyzed in order to cope with the presence of two stable structures in the gas phase, namely the all-staggered and gauche conformers. The measurements are compared to a series of Boltzmann-weighted simulations based on the momentum-space form of Kohn-Sham (B3LYP) orbital densities, and to ionization spectra obtained from high-level [ADC(3)] one-particle Green's Function calculations. Indubitable improvements in the quality of the simulated (e,2e) ionization spectra and electron momentum profiles are seen when the contributions of the gauche form of n-butane are included. Both the one-electron binding energies and momentum distributions consistently image the distortions and topological changes that molecular orbitals undergo due to torsion of the carbon backbone, and thereby exhibit variations which can be traced experimentally. With regard to the intimate relation of (e,2e) cross sections with orbital densities, electron momentum spectroscopy can therefore be viewed as a very powerful, but up to now largely unexploited, conformational probe. The study also emphasizes the influence of thermal agitation in photoionization experiments of all kind.