The Substituent Effect of the Methyl Group. Carbon 1s Ionization Energies, Proton Affinities, and Reactivities of the Methylbenzenes

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.

Same modification, different location: the mythical role of N6-adenine methylation in plant genomes

The present review summarizes recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics, discusses its importance in plant genomes, and highlights its chemical nature and functions. Adenine methylation is an epigenetic modification present in DNA (6mA) and RNA (m6A) that has a regulatory function in many cellular processes. This modification occurs through a reversible reaction that covalently binds a methyl group, usually at the N⁶ position of the purine ring. This modification carries biophysical properties that affect the stability of nucleic acids as well as their binding affinity with other molecules. DNA 6mA has been related to genome stability, gene expression, DNA replication, and repair mechanisms. Recent advances have shown that 6mA in plant genomes is related to development and stress response. In this review, we present recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics. We discuss the key elements of this modification, focusing mainly on its importance in plant genomes. Furthermore, we highlight its chemical nature and the regulatory effects that it exerts on gene expression and plant development. Finally, we emphasize the functions of 6mA in photosynthesis, stress, and flowering.

Electron delocalisation in conjugated sulfur heterocycles probed by resonant Auger spectroscopy

We propose a novel approach for an indirect probing of conjugation and hyperconjugation in core-excited molecules using resonant Auger spectroscopy. Our work demonstrates that the changes in the electronic structure of thiophene (C₄H₄S) and thiazole (C₃H₃NS), occurring in the process of resonant sulfur K-shell excitation and Auger decay, affect the stabilisation energy resulting from π-conjugation and hyperconjugation. The variations in the stabilisation energy manifest themselves in the resonant S KL_2,3L_2,3 Auger spectra of thiophene and thiazole. The comparison of the results obtained for the conjugated molecules and for thiolane (C₄H₈S), the saturated analogue of thiophene, has been performed. The experimental observations are interpreted using high-level quantum-mechanical calculations and the natural bond orbital analysis.

Positional and Conformational Isomerism in Hydroxybenzoic Acid: A Core-Level Study and Comparison with Phenol and Benzoic Acid

Three positional isomers of hydroxybenzoic acid, as well as phenol and benzoic acid, were studied using core-level photoemission and X-ray absorption spectroscopies, supported by quantum chemical calculations. While 2-hydroxybenzoic (salicylic) acid exists as a single conformer with an internal hydrogen bond, 3- and 4-hydroxybenzoic acids are mixtures of multiple conformers. The effects due to isomerism are clearly seen in the C 1s and O 1s photoelectron spectra, whereas the conformational effects on the binding energies are less pronounced. The O 1s photoelectron spectrum of salicylic acid is significantly different from that of the other two isomers, providing a signature of the hydrogen bond. In contrast, the oxygen K edge X-ray absorption spectra of the three hydroxybenzoic acids show only minor differences. The salicylic acid absorption spectrum at the carbon K edge shows a more resolved vibrational structure than the spectra of the other molecules, which can be explained in part by the existence of a single conformer. Our theoretical study of vibrational excitations in the lowest C 1s absorption bands of salicylic and 4-hydroxybenzoic acids indicates that the observed structure can be assigned to 0-0 lines of various electronic transitions since most of the totally symmetric vibrational modes with sufficiently large frequencies to be resolved are predicted to be inactive. Significant sensitivity of the C 1s excitations in 3-hydroxybenzoic acid to rotational conformerism was predicted but not observed due to spectral crowding.

Substituent effects in aqueous solutions of carboxylate salts studied by x-ray absorption spectroscopy at the oxygen K-edge

The present study aims at probing the influence of different substituents of sodium carboxylate salts R-COO^-:Na⁺ in aqueous solutions, with R = H, CH₃, C₂H₅, CH₂Cl, CF₃, and C₆H₅. X-ray absorption spectroscopy was used in the oxygen K-edge region to highlight the effect of R on the energy position of the O1s-to-π_COO* resonance of the carboxylate ion. Ab initio static exchange and ΔSCF calculations are performed and confirm the experimental observations. We qualitatively discuss the results on the basis of the polar properties of these groups as well as on the basis of the π_COO* orbital energy in the ground states, the oxygen 1s orbital ionization energy, and the O1s-to-π_COO* resonance energy.

Chlorination and tautomerism: a computational and UPS/XPS study of 2-hydroxypyridine ⇌ 2-pyridone equilibrium

The prototropic tautomeric equilibrium in 2-hydroxypyridine serves as a prototype model for the study of nucleobases' behaviour. The position of such an equilibrium in parent and chlorine monosubstituted 2-hydroxypyridine compounds in the gas phase was determined using synchrotron based techniques. The lactim tautomer is dominant for the 5- and 6-substituted compounds, whereas the parent, 3- and 4-substituted isomers have comparable populations for both tautomers. Information was obtained by measuring valence band and core level photoemission spectra at the chlorine L-edge and carbon, nitrogen, and oxygen K-edges. The effect of chlorine on the core ionization potentials of the atoms in the heterocycle was evaluated and reasonable agreement with a simple model was obtained. Basic considerations of resonance structures correctly predicts the tautomeric equilibrium for the 5- and 6-substituted compounds. The vibrationally resolved structure of the low energy portion of the valence band photoionization spectra is assigned based on quantum-chemical calculations of the neutral and charged species followed by simulation of the vibronic structure. It is shown that the first ionization occurs from a π orbital of similar shape for both tautomers. In addition, the highly distinctive vibronic structure observed just above the first ionization of the lactim, for three of the five species investigated, is assigned to the second ionization of the lactam.

Assessing GW Approaches for Predicting Core Level Binding Energies

Here we present a systematic study on the performance of different GW approaches: G₀W₀, G₀W₀ with linearized quasiparticle equation (lin-G₀W₀), and quasiparticle self-consistent GW (qsGW), in predicting core level binding energies (CLBEs) on a series of representative molecules comparing to Kohn-Sham (KS) orbital energy-based results. KS orbital energies obtained using the PBE functional are 20-30 eV lower in energy than experimental values obtained from X-ray photoemission spectroscopy (XPS), showing that any Koopmans-like interpretation of KS core level orbitals fails dramatically. Results from qsGW lead to CLBEs that are closer to experimental values from XPS, yet too large. For the qsGW method, the mean absolute error is about 2 eV, an order of magnitude better than plain KS PBE orbital energies and quite close to predictions from ΔSCF calculations with the same functional, which are accurate within ∼1 eV. Smaller errors of ∼0.6 eV are found for qsGW CLBE shifts, again similar to those obtained using ΔSCF PBE. The computationally more affordable G₀W₀ approximation leads to results less accurate than qsGW, with an error of ∼9 eV for CLBEs and ∼0.9 eV for their shifts. Interestingly, starting G₀W₀ from PBE0 reduces this error to ∼4 eV with a slight improvement on the shifts as well (∼0.4 eV). The validity of the G₀W₀ results is however questionable since only linearized quasiparticle equation results can be obtained. The present results pave the way to estimate CLBEs in periodic systems where ΔSCF calculations are not straightforward although further improvement is clearly needed.

Relationship between proton affinities and structures of proton-bound dimers

This work presents a structural approach for determination of proton affinities of molecules. In proton-bound dimer [X…H…M]⁺, M and X compete with each other to capture the proton. The correlation between proton affinities of a series of molecules, M, and X…H bond length was studied while X was a common molecule in the all proton-bound dimers. Linear relationships were observed between proton affinities of a series of alcohols, ethers, aldehydes, ketones and amines and X…H bond length, where H₂O and HF were used as X. The method was employed for the measurement of proton affinities of (HF)_1-10 clusters using NH₃ and H₂O as common molecules, [NH₃…H…(HF)_n]⁺ and [H₂O…H…(HF)_n]⁺. A linear correlation was observed for the PAs of (HF)_n clusters versus N…H bond length.

Effect of the Number of Methyl Groups on the Cation Affinity of Oxygen, Nitrogen, and Phosphorus Sites of Lewis Bases

The effect of number of CH₃ groups (n) on the cation (H⁺, Li⁺, Na⁺, Al⁺, CH₃⁺) affinity, polarizability, and dipole moment of 14 simple molecules was investigated. Linear correlations were observed between the polarizabilities and the number of methyl groups. The variations of the cation affinities and dipole moments with the number of methyl groups (n) were not linear, and a quadratic function was proposed for obtaining a good fit of the experimental data. Also, because the proton affinities (PA), lithium cation affinities (LCA), sodium cation affinities (SCA), aluminum cation affinity (AlCA), and methyl cation affinity (MCA) varied quadratically with polarizabilities (α), a formula of the form [cation affinities] = a + bα + cα² was proposed. After correction of the PAs, LCAs, SCAs, AlCA, and MCA for the dipole/charge interaction (E_μ), linear relationships were observed between the corrected cation affinities and n or α. The contribution of E_μ to PA and MCA was small (less than 20%), and its contribution to LCA and SCA was large (>50%). The electrostatic contribution to AlCA was considerable (20-50%); however, it was smaller than the electrostatic contribution to LCA and SCA.

Performance of the TPSS Functional on Predicting Core Level Binding Energies of Main Group Elements Containing Molecules: A Good Choice for Molecules Adsorbed on Metal Surfaces

Here we explored the performance of Hartree-Fock (HF), Perdew-Burke-Ernzerhof (PBE), and Tao-Perdew-Staroverov-Scuseria (TPSS) functionals in predicting core level 1s binding energies (BEs) and BE shifts (ΔBEs) for a large set of 68 molecules containing a wide variety of functional groups for main group elements B → F and considering up to 185 core levels. A statistical analysis comparing with X-ray photoelectron spectroscopy (XPS) experiments shows that BEs estimations are very accurate, TPSS exhibiting the best performance. Considering ΔBEs, the three methods yield very similar and excellent results, with mean absolute deviations of ∼0.25 eV. When considering relativistic effects, BEs deviations drop approaching experimental values. So, the largest mean percentage deviation is of 0.25% only. Linear trends among experimental and estimated values have been found, gaining offsets with respect to ideality. By adding relativistic effects to offsets, HF and TPSS methods underestimate experimental values by solely 0.11 and 0.05 eV, respectively, well within XPS chemical precision. TPSS is posed as an excellent choice for the characterization, by XPS, of molecules on metal solid substrates, given its suitability in describing metal substrates bonds and atomic and/or molecular orbitals.

Conformations and CH/π interactions in aliphatic alkynes and alkenes

The carbon 1s photoelectron spectra of a series of aliphatic alkynes and alkenes that have the possibility of possessing two or more conformers have been recorded with high resolution. The two conformers of 2-hexyne and 4-methyl-1-pentyne, anti and gauche, have been identified and quantified from an analysis of their carbon 1s photoelectron spectra, yielding 30 ± 5% and 70 ± 6% anti conformers, respectively. In the case of 1-hexyne, the photoelectron spectrum is shown to provide partial information on the distribution of conformers. Central to these analyses is a pronounced ability of the C1s photoemission process to distinguish between conformers that display weak γ-CH/π hydrogen bonding and those that do not. For the corresponding alkene analogs, similar analyses of their C1s photoelectron spectra do not lead to conclusive information on the conformational equilibria, mainly because of significantly smaller chemical shifts and higher number of conformers compared with the alkynes.

Single and double core-hole ionization energies in molecules

The recently demonstrated ability to measure double-hole core-ionization energies in first-row elements has led to a renewed interest in the use of such energies to investigate the effects of initial-state charge distribution and final-state charge rearrangement on the energies of chemical processes that involve addition of charge to a molecule. With theoretical calculations for the molecules CH(4-n)X(n), X = F, Cl, and for C(CH(3))(4) as a basis, the relationships between one-hole and two-hole ionization energies, on one hand, and initial-state and final-state effects, on the other, are reviewed. It is shown that higher-order corrections to the traditionally used relationships are quantitatively significant but do not lead to qualitatively different conclusions. The role of the Wagner plot as a way to display the relationships among the various quantities of interest is discussed, and a generalized Wagner plot for displaying two-site double-hole ionization energies is presented. Some possible applications of measurements of double-hole ionization energies to the investigation of molecular conformation and molecular fragmentation are discussed.