A theoretical and experimental study of the near edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectra (XPS) of nucleobases: Thymine and adenine

Time-resolved x-ray spectroscopy of nucleobases and their thionated analogs

The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.

Effect of Protonation on the Molecular Structure of Adenosine 5'-Triphosphate: A Combined Theoretical and Near Edge X-ray Absorption Fine Structure Study

The present work combines the near edge X-ray absorption mass spectrometry of a protonated adenosine 5'-triphosphate (ATP) molecule isolated in an ion trap with (time-dependent) density functional theory calculations. Our study unravels the effect of protonation on the ATP structure and its spectral properties, providing structure-property relationships at atomistic resolution for protonated ATP (ATPH) isolated in the gas-phase conditions. On the other hand, the present C and N K-edge X-ray absorption spectra of isolated ATPH appear closely like those previously reported for solvated ATP at low pH. Therefore, the present work should be relevant for further investigation and modeling of structure-function properties of protonated adenine and ATP in complex biological environments.

Fractional-Electron and Transition-Potential Methods for Core-to-Valence Excitation Energies Using Density Functional Theory

Methods for computing X-ray absorption spectra based on a constrained core hole (possibly containing a fractional electron) are examined. These methods are based on Slater's transition concept and its generalizations, wherein core-to-valence excitation energies are determined using Kohn-Sham orbital energies. Methods examined here avoid promoting electrons beyond the lowest unoccupied molecular orbital, facilitating robust convergence. Variants of these ideas are systematically tested, revealing a best-case accuracy of 0.3-0.4 eV (with respect to experiment) for K-edge transition energies. Absolute errors are much larger for higher-lying near-edge transitions but can be reduced below 1 eV by introducing an empirical shift based on a charge-neutral transition-potential method, in conjunction with functionals such as SCAN, SCAN0, or B3LYP. This procedure affords an entire excitation spectrum from a single fractional-electron calculation, at the cost of ground-state density functional theory and without the need for state-by-state calculations. This shifted transition-potential approach may be especially useful for simulating transient spectroscopies or in complex systems where excited-state Kohn-Sham calculations are challenging.

Algebraic Diagrammatic Construction Theory for Simulating Charged Excited States and Photoelectron Spectra

Charged excitations are electronic transitions that involve a change in the total charge of a molecule or material. Understanding the properties and reactivity of charged species requires insights from theoretical calculations that can accurately describe orbital relaxation and electron correlation effects in open-shell electronic states. In this Review, we describe the current state of algebraic diagrammatic construction (ADC) theory for simulating charged excitations and its recent developments. We start with a short overview of ADC formalism for the one-particle Green's function, including its single- and multireference formulations and extension to periodic systems. Next, we focus on the capabilities of ADC methods and discuss recent findings about their accuracy for calculating a wide range of excited-state properties. We conclude our Review by outlining possible directions for future developments of this theoretical approach.

Photoionization Dynamics and Proton Transfer within the Adenine-Thymine Nucleobase Pair

Studying the stability of hydrogen-bonded nucleobase pairs, at the heart of the genetic code, is of utmost importance for an in-depth understanding of basic mechanisms of life and biomolecular evolution. We present here a VUV single photon ionization dynamic study of the nucleobase pair adenine-thymine (AT), revealing its ionization and dissociative ionization thresholds via double imaging electron/ion coincidence spectroscopy. The experimental data, consisting of cluster mass-resolved threshold photoelectron spectra and photon energy-dependent ion kinetic energy release distributions, allow the unambiguous distinction of the dissociation of AT into protonated adenine AH⁺ and a dehydrogenated thymine radical T(-H) from dissociative ionization processes of other nucleobase clusters. Comparison to high-level ab initio calculations indicates that our experimental observations can be explained by a single hydrogen-bonded conformer present in our molecular beam and allows the estimation of an upper limit of the barrier of the proton transfer in the ionized AT pair.

A study of core-excited states of organic molecules computed with the generalized active space driven similarity renormalization group

This work examines the accuracy and precision of x-ray absorption spectra computed with a multireference approach that combines generalized active space (GAS) references with the driven similarity renormalization group (DSRG). We employ the x-ray absorption benchmark of organic molecule (XABOOM) set, consisting of 116 transitions from mostly organic molecules [Fransson et al., J. Chem. Theory Comput. 17, 1618 (2021)]. Several approximations to a full-valence active space are examined and benchmarked. Absolute excitation energies and intensities computed with the GAS-DSRG truncated to second-order in perturbation theory are found to systematically underestimate experimental and reference theoretical values. Third-order perturbative corrections significantly improve the accuracy of GAS-DSRG absolute excitation energies, bringing the mean absolute deviation from experimental values down to 0.32 eV. The ozone molecule and glyoxylic acid are particularly challenging for second-order perturbation theory and are examined in detail to assess the importance of active space truncation and intruder states.

Slater transition methods for core-level electron binding energies

Methods for computing core-level ionization energies using self-consistent field (SCF) calculations are evaluated and benchmarked. These include a "full core hole" (or "ΔSCF") approach that fully accounts for orbital relaxation upon ionization, but also methods based on Slater's transition concept in which the binding energy is estimated from an orbital energy level that is obtained from a fractional-occupancy SCF calculation. A generalization that uses two different fractional-occupancy SCF calculations is also considered. The best of the Slater-type methods afford mean errors of 0.3-0.4 eV with respect to experiment for a dataset of K-shell ionization energies, a level of accuracy that is competitive with more expensive many-body techniques. An empirical shifting procedure with one adjustable parameter reduces the average error below 0.2 eV. This shifted Slater transition method is a simple and practical way to compute core-level binding energies using only initial-state Kohn-Sham eigenvalues. It requires no more computational effort than ΔSCF and may be especially useful for simulating transient x-ray experiments where core-level spectroscopy is used to probe an excited electronic state, for which the ΔSCF approach requires a tedious state-by-state calculation of the spectrum. As an example, we use Slater-type methods to model x-ray emission spectroscopy.

Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides

Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L- and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy. The combination of absorption site selectivity and photoproduct sensitivity allowed the identification of X-ray spectral signatures of specific processes. Moreover, charge and/or energy as well as H transfer from the backbone to nucleobases has been directly observed. Although the probability of one versus two H transfer following valence ionization depends on the nucleobase, ionization of sugar or phosphate groups at the carbon K-edge or the phosphorus L-edge mainly leads to single H transfer to protonated adenine. Moreover, our results indicate a surprising proton-transfer process to specifically form protonated guanine after excitation or ionization of P 2p electrons.

Spectroscopic and quantum mechanical study of a scavenger molecule: N,N-diethylhydroxylamine

We report a combination of quantum mechanical calculations and a range of spectroscopic measurements in the gas phase of N,N-diethylhydroxylamine, an important scavenger compound. Three conformers were observed by pulsed jet Fourier transform microwave spectroscopy in the 6.5-18.5 GHz frequency range. They are characterized by the hydroxyl hydrogen atom being in trans orientation with respect to the bisector of the CNC angle while the side alkyl chains can be both trans (global minimum, C_s symmetry, A = 7608.1078(4), B = 2020.2988(2) and C = 1760.5423(2) MHz) or one trans and the other gauche (second energy minimum, A = 5302.896(1), B = 2395.9822(4) and C = 1804.8567(3) MHz) or gauche' (third energy minimum, A = 5960.8025(6), B = 2273.6627(4) and C = 1975.8074(4) MHz). For the global minimum, the ¹³C_α,¹³C_β and ¹⁵N isotopologues were observed in natural abundance, allowing for an accurate partial structure determination. Moreover, several lines were detected by free jet absorption millimeter wave spectroscopy in the 59.6-74.4 GHz spectral range. The electron binding energies of the highest occupied molecular orbital and the next-to-highest occupied molecular orbital, determined by photoelectron spectroscopy, are 8.95 and 10.76 eV, respectively. Supporting calculations evidence that, (i) upon ionization of the HOMO, the molecular structure changes from an amine to an N-oxoammonium arrangement and (ii) the 0-0 of the HOMO-1 photoionization is 10.46 eV. The K-shell binding energies, determined by X-ray photoelectron spectroscopy, are 290.42 eV (C_β), 291.45 eV (C_α), 405.98 eV (N) and 538.75 eV (O). The Fourier transform near infrared spectrum is reported and a tentative assignment is proposed. The equilibrium wavenumber (ω̃ = 3811 cm^-1) and the anharmonicity constant (ω̃χ = -87.5 cm^-1) of the hydroxyl stretching mode were estimated using a quadratic model.

Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory for Accurate X-ray Absorption Spectroscopy

It is demonstrated that the challenging core-hole particle (CHP) orbital relaxation for core electron spectra can be readily achieved by the mixed-reference spin-flip (MRSF)-time-dependent density functional theory (TDDFT). With the additional scalar relativistic effects on K-edge excitation energies of 24 second- and 17 third-row molecules, the particular ΔCHP-MRSF(R) exhibited near perfect predictions with RMSE ∼0.5 eV, featuring a median value of 0.3 and an interquartile range of 0.4. Overall, the CHP effect is 2-4 times stronger than relativistic ones, contributing more than 20 eV in the cases of sulfur and chlorine third-row atoms. Such high precision allows to explain the splitting and spectral shapes of O, N, and C atom K-edges in the ground state of thymine with atom as well as orbital specific accuracy. The same protocol with a double hole particle relaxation also produced remarkably accurate K-edge spectra of core to valence hole excitation energies from the first (n_O8π*) and second (ππ*) excited states of thymine, confirming the assignment of 1s → n excitation for the experimentally observed 526.4 eV peak. Regarding both accuracy and practicality, therefore, MRSF-TDDFT provides a promising protocol for core electron spectra of both ground and excited electronic states alike.

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.

Computing x-ray absorption spectra from linear-response particles atop optimized holes

State specific orbital optimized density functional theory (OO-DFT) methods, such as restricted open-shell Kohn-Sham (ROKS), can attain semiquantitative accuracy for predicting x-ray absorption spectra of closed-shell molecules. OO-DFT methods, however, require that each state be individually optimized. In this Communication, we present an approach to generate an approximate core-excited state density for use with the ROKS energy ansatz, which is capable of giving reasonable accuracy without requiring state-specific optimization. This is achieved by fully optimizing the core-hole through the core-ionized state, followed by the use of electron-addition configuration interaction singles to obtain the particle level. This hybrid approach can be viewed as a DFT generalization of the static-exchange (STEX) method and can attain ∼0.6 eV rms error for the K-edges of C-F through the use of local functionals, such as PBE and OLYP. This ROKS(STEX) approach can also be used to identify important transitions for full OO ROKS treatment and can thus help reduce the computational cost of obtaining OO-DFT quality spectra. ROKS(STEX), therefore, appears to be a useful technique for the efficient prediction of x-ray absorption spectra.

Surface-Induced Keto-Enol Tautomerization of DNA Base Molecules and Consequent [4 + 2]-like Cycloaddition on Si(111)7×7

Adsorption and film growth of deoxyribonucleic acid (DNA) base molecules (cytosine, guanine, thymine, and adenine) on Si(111)7×7 have been studied by combining X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). Multiple tautomeric forms and keto-enol tautomerization are revealed by the O 1s, N 1s, and C 1s XPS spectra of the O-containing DNA bases: cytosine, guanine, and thymine. While the carbonyl group-containing keto tautomer is more stable in a thick film and in powder, the hydroxyl group-containing enol tautomer is found at the interface. The keto-enol tautomerization, as induced by the reactive Si(111)7×7 surface, leads to the formation of a conjugated aromatic six-membered ring with a delocalized π electron system and to the consequent [4 + 2]-like cycloaddition between the enol tautomer and the 7×7 surface. The DFT calculation suggests that the enol tautomer exhibits a kinetic advantage over the keto one for the [4 + 2]-like cycloaddition. Among the several plausible pathways for the cycloaddition provided by the enol tautomer, the experimentally determined one involves a ring N and ring C atom (a polar pair), rather than two ring C atoms (a nonpolar pair), to better match the polar Si adatom-restatom pair of the 7×7 surface. Furthermore, the reacted ring C atom does not have any attached terminal functional group (e.g., -NH₂ and -OH). Further deposition leads to continuous film growth in the keto tautomeric form for cytosine and guanine. For the only O-free DNA base molecule, adenine, dative bonding N → Si, rather than the [4 + 2]-like cycloaddition, is observed on the 7×7 surface. Of the four DNA base molecules, adenine is also the only one with its aromaticity maintained when adsorbed on the Si(111)7×7 surface. A reactive surface like the 7×7 surface could therefore provide a new control to trigger tautomerization that is often associated with genetic mutation.

A Core-Valence Separated Similarity Transformed EOM-CCSD Method for Core-Excitation Spectra

We present the theory and implementation of a core-valence separated similarity transformed EOM-CCSD (STEOM-CCSD) method for K-edge core excitation spectra. The method can select an appropriate active space using CIS natural orbitals and near "black box" to use. The second similarity transformed Hamiltonian is diagonalized in the space of single excitation. Therefore, the final diagonalization step is free from the convergence problem arising due to the coupling of the core-excited states with the continuum of doubly excited states. Convergence trouble can appear for the preceding core-ionized state calculation in STEOM-CCSD. A core-valence separation (CVS) scheme compatible with the natural orbital based active space selection (CVS-STEOM-CCSD-NO) is implemented to overcome the problem. The CVS-STEOM-CCSD-NO has a similar accuracy to that of the standard CVS-EOM-CCSD method but comes with a lower computational cost. The modification required in the CVS scheme to make use of the CIS natural orbital is highlighted. The suitability of the CVS-STEOM-CCSD-NO method for chemical application is demonstrated by simulating the K-edge spectra of glycine and thymine.

X-ray photoemission studies of the interaction of metals and metal ions with DNA

X-ray Photoelectron Spectroscopy (XPS) has been used to study the interactions of heavy metal ions with DNA with some success. Surface sensitivity and selectivity of XPS are advantageous for identifying and characterizing the chemical and elemental structure of the DNA to metal interaction. This review summarizes the status of what amounts to a large part of the photoemission investigations of biomolecule interactions with metals and offers insight into the mechanism for heavy metal-bio interface interactions. Specifically, it is seen that metal interaction with DNA results in conformational changes in the DNA structure.

Equation of motion coupled-cluster study of core excitation spectra II: Beyond the dipole approximation

We present the time-independent (TI) and time-dependent (TD) equation of motion coupled-cluster (EOM-CC) oscillator strengths not limited to those obtained by the dipole approximation. For the conventional TI-EOM-CC, we implement all the terms in the multipole expansion through second order that contributes to the oscillator strength. These include contributions such as magnetic dipole, electric quadrupole, electric octupole, and magnetic quadrupole. In TD-EOM-CC, we only include the quadrupole moment contributions. This augments our previous work [Y. C. Park, A. Perera, and R. J. Bartlett, J. Chem. Phys. 151, 164117 (2019)]. The inclusion of the quadrupole contributions (and all the other contributions through second order in the case of TI-EOM-CCSD) enables us to obtain the intensities for the pre-edge transitions in the metal K-edge spectra, which are dipole inactive. The TI-EOM-CCSD and TD-EOM-CCSD spectra of Ti⁴⁺ atoms are used to showcase the implementation of the second-order oscillator strengths. The origin of 1s → e and 1s → t₂ in core spectra from iron tetrachloride and titanium tetrachloride is discussed and compared with the experiment.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

Analytical gradients for core-excited states in the algebraic diagrammatic construction (ADC) framework

Expressions for analytical molecular gradients of core-excited states have been derived and implemented for the hierarchy of algebraic diagrammatic construction (ADC) methods up to extended second-order within the core-valence separation (CVS) approximation. We illustrate the use of CVS-ADC gradients by determining relaxed core-excited state potential energy surfaces and optimized geometries for water, formic acid, and benzene. For water, our results show that in the dissociative lowest core-excited state, a linear configuration is preferred. For formic acid, we find that the O K-edge lowest core-excited state is non-planar, a fact that is not captured by the equivalent core approximation where the core-excited atom with its hole is replaced by the "Z + 1" neighboring atom in the periodic table. For benzene, the core-excited state gradients are presented along the Jahn-Teller distorted geometry of the 1s → π* excited state. Our development may pave a new path to studying the dynamics of molecules in their core-excited states.

Transient resonant Auger-Meitner spectra of photoexcited thymine

We present the first investigation of excited state dynamics by resonant Auger-Meitner spectroscopy (also known as resonant Auger spectroscopy) using the nucleobase thymine as an example. Thymine is photoexcited in the UV and probed with X-ray photon energies at and below the oxygen K-edge. After initial photoexcitation to a ππ* excited state, thymine is known to undergo internal conversion to an nπ* excited state with a strong resonance at the oxygen K-edge, red-shifted from the ground state π* resonances of thymine (see our previous study Wolf, et al., Nat. Commun., 2017, 8, 29). We resolve and compare the Auger-Meitner electron spectra associated both with the excited state and ground state resonances, and distinguish participator and spectator decay contributions. Furthermore, we observe simultaneously with the decay of the nπ* state signatures the appearance of additional resonant Auger-Meitner contributions at photon energies between the nπ* state and the ground state resonances. We assign these contributions to population transfer from the nπ* state to a ππ* triplet state via intersystem crossing on the picosecond timescale based on simulations of the X-ray absorption spectra in the vibrationally hot triplet state. Moreover, we identify signatures from the initially excited ππ* singlet state which we have not observed in our previous study.

Site-selective soft X-ray absorption as a tool to study protonation and electronic structure of gas-phase DNA

The conformation and the electronic structure of gas-phase oligonucleotides depends strongly on the protonation site. 5'-d(FUAG) can either be protonated at the A-N1 or at the G-N7 position. We have stored protonated 5'-d(FUAG) cations in a cryogenic ion trap held at about 20 K. To identify the protonation site and the corresponding electronic structure, we have employed soft X-ray absorption spectroscopy at the nitrogen K-edge. The obtained spectra were interpreted by comparison to time-dependent density functional theory calculations using a short-range exchange correlation functional. Despite the fact that guanine has a significantly higher proton affinity than adenine, the agreement between experiment and theory is better for the A-N1 protonated system. Furthermore, an inverse site sensitivity is observed in which the yield of the nucleobase fragments that contain the absorption site appears substantially reduced, which could be explained by non-statistical fragmentation processes, localized on the photoabsorbing nucleobase.

Orbital Optimized Density Functional Theory for Electronic Excited States

Density functional theory (DFT) based modeling of electronic excited states is of importance for investigation of the photophysical/photochemical properties and spectroscopic characterization of large systems. The widely used linear response time-dependent DFT (TDDFT) approach is, however, not effective at modeling many types of excited states, including (but not limited to) charge-transfer states, doubly excited states, and core-level excitations. In this perspective, we discuss state-specific orbital optimized (OO) DFT approaches as an alterative to TDDFT for electronic excited states. We motivate the use of OO-DFT methods and discuss reasons behind their relatively restricted historical usage (vs TDDFT). We subsequently highlight modern developments that address these factors and allow efficient and reliable OO-DFT computations. Several successful applications of OO-DFT for challenging electronic excitations are also presented, indicating their practical efficacy. OO-DFT approaches are thus increasingly becoming a useful route for computing excited states of large chemical systems. We conclude by discussing the limitations and challenges still facing OO-DFT methods, as well as some potential avenues for addressing them.

XABOOM: An X-ray Absorption Benchmark of Organic Molecules Based on Carbon, Nitrogen, and Oxygen 1s → π* Transitions

The performance of several standard and popular approaches for calculating X-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges of 40 primarily organic molecules up to the size of guanine has been evaluated, focusing on the low-energy and intense 1s → π* transitions. Using results obtained with CVS-ADC(2)-x and fc-CVS-EOM-CCSD as benchmark references, we investigate the performance of CC2, ADC(2), ADC(3/2), and commonly adopted density functional theory (DFT)-based approaches. Here, focus is on precision rather than on accuracy of transition energies and intensities-in other words, we target relative energies and intensities and the spread thereof, rather than absolute values. The use of exchange-correlation functionals tailored for time-dependent DFT calculations of core excitations leads to error spreads similar to those seen for more standard functionals, despite yielding superior absolute energies. Long-range corrected functionals are shown to perform particularly well compared to our reference data, showing error spreads in energy and intensity of 0.2-0.3 eV and ∼10%, respectively, as compared to 0.3-0.6 eV and ∼20% for a typical pure hybrid. In comparing intensities, state mixing can complicate matters, and techniques to avoid this issue are discussed. Furthermore, the influence of basis sets in high-level ab initio calculations is investigated, showing that reasonably accurate results are obtained with the use of 6-311++G**. We name this benchmark suite as XABOOM (X-ray absorption benchmark of organic molecules) and provide molecular structures and ground-state self-consistent field energies and spectroscopic data. We believe that it provides a good assessment of electronic structure theory methods for calculating X-ray absorption spectra and will become useful for future developments in this field.

Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry

Near-edge X-ray absorption mass spectrometry (NEXAMS) is an action-spectroscopy technique of growing interest for investigations into the spatial and electronic structure of biomolecules. It has been used successfully to give insights into different aspects of the photodissociation of peptides and to probe the conformation of proteins. It is a current question whether the fragmentation pathways are sensitive toward effects of conformational isomerism, tautomerism, and intramolecular interactions in gas-phase peptides. To address this issue, we studied the cationic fragments of cryogenically cooled gas-phase leucine enkephalin ([LeuEnk+H]⁺) and methionine enkephalin ([MetEnk+H]⁺) produced upon soft X-ray photon absorption at the carbon, nitrogen, and oxygen K-edges. The interpretation of the experimental ion yield spectra was supported by density-functional theory and restricted-open-shell configuration interaction with singles (DFT/ROCIS) calculations. The analysis revealed several effects that could not be rationalized based on the peptide's amino acid sequences alone. Clear differences between the partial ion yields measured for both peptides upon C 1s → π*(C═C) excitations in the aromatic amino acid side chains give evidence for a sulfur-aromatic interaction between the methionine and phenylalanine side chain of [MetEnk+H]⁺. Furthermore, a peak associated with N 1s → π*(C═N) transitions, linked to a tautomeric keto-to-enol conversion of peptide bonds, was only present in the photon energy resolved ion yield spectra of [MetEnk+H]⁺.

An assessment of different electronic structure approaches for modeling time-resolved x-ray absorption spectroscopy

We assess the performance of different protocols for simulating excited-state x-ray absorption spectra. We consider three different protocols based on equation-of-motion coupled-cluster singles and doubles, two of them combined with the maximum overlap method. The three protocols differ in the choice of a reference configuration used to compute target states. Maximum-overlap-method time-dependent density functional theory is also considered. The performance of the different approaches is illustrated using uracil, thymine, and acetylacetone as benchmark systems. The results provide guidance for selecting an electronic structure method for modeling time-resolved x-ray absorption spectroscopy.

Equation-of-Motion MLCCSD and CCSD-in-HF Oscillator Strengths and Their Application to Core Excitations

We present an implementation of equation-of-motion oscillator strengths for the multilevel CCSD (MLCCSD) model where CCS is used as the lower level method (CCS/CCSD). In this model, the double excitations of the cluster operator are restricted to an active orbital space, whereas the single excitations are unrestricted. Calculated nitrogen K-edge spectra of adenosine, adenosine triphosphate (ATP), and an ATP-water system are used to demonstrate the performance of the model. Projected atomic orbitals (PAOs) are used to partition the virtual space into active and inactive orbital sets. Cholesky decomposition of the Hartree-Fock density is used to partition the occupied orbitals. This Cholesky-PAO partitioning is cheap, scaling as O(N3), and is suitable for the calculation of core excitations, which are localized in character. By restricting the single excitations of the cluster operator to the active space, as well as the double excitations, the CCSD-in-HF model is obtained. A comparison of the two models-MLCCSD and CCSD-in-HF-is presented for the core excitation spectra of the adenosine and ATP systems.

PSIXAS: A Psi4 plugin for efficient simulations of X-ray absorption spectra based on the transition-potential and Δ-Kohn-Sham method

Near edge X-ray absorption fine structure (NEXAFS) spectra and their pump-probe extension (PP-NEXAFS) offer insights into valence- and core-excited states. We present PSIXAS, a recent implementation for simulating NEXAFS and PP-NEXAFS spectra by means of the transition-potential and the Δ-Kohn-Sham method. The approach is implemented in form of a software plugin for the Psi4 code, which provides access to a wide selection of basis sets as well as density functionals. We briefly outline the theoretical foundation and the key aspects of the plugin. Then, we use the plugin to simulate PP-NEXAFS spectra of thymine, a system already investigated by others and us. It is found that larger, extended basis sets are needed to obtain more accurate absolute resonance positions. We further demonstrate that, in contrast to ordinary NEXAFS simulations, where the choice of the density functional plays a minor role for the shape of the spectrum, for PP-NEXAFS simulations the choice of the density functional is important. Especially hybrid functionals (which could not be used straightforwardly before to simulate PP-NEXAFS spectra) and their amount of "Hartree-Fock like" exact exchange affects relative resonance positions in the spectrum.

Generalized single excitation configuration interaction: an investigation into the impact of the inclusion of non-orthogonality on the calculation of core-excited states

In this paper, we investigate different non-orthogonal generalizations of the configuration interaction with single substitutions (CIS) method and their impact on the calculation of core-excited states.

Dyson orbitals within the fc-CVS-EOM-CCSD framework: theory and application to X-ray photoelectron spectroscopy of ground and excited states

Ionization energies and Dyson orbitals within frozen-core core–valence separated equation-of-motion coupled cluster singles and doubles (fc-CVS-EOM-CCSD) enable efficient and reliable calculations of standard XPS and of UV-pump/XPS probe spectra.

Equation of motion coupled-cluster for core excitation spectra: Two complementary approaches

This paper presents core excitation spectra from coupled-cluster (CC) theory obtained from both a time-independent and a new time-dependent formalism. The conventional time-independent CC formulation for excited states is the equation-of-motion (EOM-CC) method whose eigenvalues and eigenvectors describe the core excited states. An alternative computational procedure is offered by a time-dependent CC description. In that case, the dipole transition operator is expressed in the CC effective Hamiltonian form and propagated with respect to time. The absorption spectrum is obtained from the CC dipole autocorrelation function via a Fourier transformation. Comparisons are made among the time-dependent results obtained from second-order perturbation theory, to coupled cluster doubles and their linearized forms (CCD and LCCD), to CC singles and doubles (CCSD) and the linearized form (LCCSD). In the time-independent case, considerations of triples (EOM-CCSDT) and quadruples (EOM-CCSDTQ) are used to approach sub-electron volt accuracy. A particular target is the allyl radical, as an example of an open-shell molecule. As the results have to ultimately be the same, the two procedures offer a complementary approach toward analyzing experimental results.

Photochemical pathways in nucleobases measured with an X-ray FEL

The conversion of light energy into other molecular energetic degrees of freedom is often dominated by ultrafast, non-adiabatic processes. Femtosecond spectroscopy with optical pulses has helped in shaping our understanding of crucial processes in molecular energy-conversion. The advent of new, ultrashort and bright X-ray free electron laser sources opens the possibility to use X-ray-typical element and site sensitivity for ultrafast molecular research. We present two types of spectroscopy, ultrafast Auger and ultrafast X-ray absorption spectroscopy, and discuss their sensitivity to molecular processes. While Auger spectroscopy is able to monitor bond distance changes in the vicinity of an X-ray created core hole, near-edge absorption spectroscopy can deliver high-fidelity information on non-adiabatic transitions involving lone-pair orbitals. We demonstrate these features on the example of the UV-excited nucleobase thymine, investigated at the oxygen K-edge. We find a C-O bond elongation in the Auger data in addition to ππ*/ nπ* non-adiabatic transition in X-ray near-edge absorption. We compare the results from both methods and draw a conclusive scenario of non-adiabatic molecular relaxation after UV excitation. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.

New and Efficient Equation-of-Motion Coupled-Cluster Framework for Core-Excited and Core-Ionized States

We present a fully analytical implementation of the core-valence separation (CVS) scheme for the equation-of-motion (EOM) coupled-cluster singles and doubles (CCSD) method for calculations of core-level states. Inspired by the CVS idea as originally formulated by Cederbaum, Domcke, and Schirmer, pure valence excitations are excluded from the EOM target space and the frozen-core approximation is imposed on the reference-state amplitudes and multipliers. This yields an efficient, robust, practical, and numerically balanced EOM-CCSD framework for calculations of excitation and ionization energies as well as state and transition properties (e.g., spectral intensities, natural transition, and Dyson orbitals) from both the ground and excited states. The errors in absolute excitation/ionization energies relative to the experimental reference data are on the order of 0.2-3.0 eV, depending on the K-edge considered and on the basis set used, and the shifts are systematic for each edge. Compared to a previously proposed CVS scheme where CVS was applied as a posteriori projection only during the solution of the EOM eigenvalue equations, the new scheme is computationally cheaper. It also achieves better cancellation of errors, yielding similar spectral profiles but with absolute core excitation and ionization energies that are systematically closer to the corresponding experimental data. Among the presented results are calculations of transient-state X-ray absorption spectra, relevant for interpretation of UV-pump/X-ray probe experiments.

Modeling core-level excitations with variationally optimized reduced-density matrices and the extended random phase approximation

The information contained within ground-state one- and two-electron reduced-density matrices (RDMs) can be used to compute wave functions and energies for electronically excited states through the extended random phase approximation (ERPA). The ERPA is an appealing framework for describing excitations out of states obtained via the variational optimization of the two-electron RDM (2-RDM), as the variational 2-RDM (v2RDM) approach itself can only be used to describe the lowest-energy state of a given spin symmetry. The utility of the ERPA for predicting near-edge features relevant to x-ray absorption spectroscopy is assessed for the case that the 2-RDM is obtained from a ground-state v2RDM-driven complete active space self-consistent field (CASSCF) computation. A class of killer conditions for the CASSCF-specific ERPA excitation operator is derived, and it is demonstrated that a reliable description of core-level excitations requires an excitation operator that fulfills these conditions; the core-valence separation (CVS) scheme yields such an operator. Absolute excitation energies evaluated within the CASSCF/CVS-ERPA framework are slightly more accurate than those obtained from the usual random phase approximation (RPA), but the CVS-ERPA is not more accurate than RPA for predicting the relative positions of near-edge features. Nonetheless, CVS-ERPA is established as a reasonable starting point for the treatment of core-level excitations using variationally optimized 2-RDMs.

Green's function coupled cluster formulations utilizing extended inner excitations

In this paper, we analyze new approximations of the Green's function coupled cluster (GFCC) method where locations of poles are improved by extending the excitation level of inner auxiliary operators. These new GFCC approximations can be categorized as the GFCC-i(n, m) method, where the excitation level of the inner auxiliary operators (m) used to describe the ionization potential and electron affinity effects in the N - 1 and N + 1 particle spaces is higher than the excitation level (n) used to correlate the ground-state coupled cluster wave function for the N-electron system. Furthermore, we reveal the so-called "n + 1" rule in this category [or the GFCC-i(n, n + 1) method], which states that in order to maintain size-extensivity of the Green's function matrix elements, the excitation level of inner auxiliary operators X _p (ω) and Y _q (ω) cannot exceed n + 1. We also discuss the role of the moments of coupled cluster equations that in a natural way assures these properties. Our implementation in the present study is focused on the first approximation in this GFCC category, i.e., the GFCC-i(2,3) method. As our first practice, we use the GFCC-i(2,3) method to compute the spectral functions for the N₂ and CO molecules in the inner and outer valence regimes. In comparison with the Green's function coupled cluster singles, doubles results, the computed spectral functions from the GFCC-i(2,3) method exhibit better agreement with the experimental results and other theoretical results, particularly in terms of providing higher resolution of satellite peaks and more accurate relative positions of these satellite peaks with respect to the main peak positions.

Births in the United States, 2017

This report presents selected highlights from 2017 final birth data on key demographic, health care utilization, and infant health indicators. General fertility rates (the number of births per 1,000 females aged 15-44 years) and teen birth rates are presented by race and Hispanic origin. The use of Medicaid as the source of payment for the delivery and preterm birth rates are presented by the age of the mother. Data for 2017 are compared with 2016 for each indicator.

Green's Function Coupled-Cluster Approach: Simulating Photoelectron Spectra for Realistic Molecular Systems

In this paper, we present an efficient implementation for the analytical energy-dependent Green's function coupled-cluster with singles and doubles (GFCCSD) approach with our first practice being computing spectral functions of realistic molecular systems. Because of its algebraic structure, the presented method is highly scalable and is capable of computing spectral function for a given molecular system in any energy region. Several typical examples have been given to demonstrate its capability of computing spectral functions not only in the valence band but also in the core-level energy region. Satellite peaks have been observed in the inner valence band and core-level energy region where a many-body effect becomes significant and the single particle picture of ionization often breaks down. The accuracy test has been carried out by extensively comparing the computed spectral functions by our GFCCSD method with experimental photoelectron spectra as well as the theoretical ionization potentials obtained from other methods. It turns out the GFCCSD method is able to provide a qualitative or semiquantitative level of description of ionization processes in both the core and valence regimes. To significantly improve the GFCCSD results for the main ionic states, a larger basis set can usually be employed, whereas the improvement of the GFCCSD results for the satellite states needs higher-order many-body terms to be included in the GFCC implementation.

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.