Proton-Coupled Electron Transfer and Hydrogen Tunneling in Olive Oil Phenol Reactions.

Olive oil phenols are recognized as molecules with numerous positive health effects, many of which rely on their antioxidative activity, i.e., the ability to transfer hydrogen to radicals. Proton-coupled electron transfer reactions and hydrogen tunneling are ubiquitous in biological systems. Reactions of olive oil phenols, hydroxytyrosol, tyrosol, oleuropein, oleacein, oleocanthal, homovanillyl alcohol, vanillin, and a few phenolic acids with a DPPH• (2,2-diphenyl-1-picrylhydrazyl) radical in a 1,4-dioxane:water = 95:5 or 99:1 v/v solvent mixture were studied through an experimental kinetic analysis and computational chemistry calculations. The highest rate constants corresponding to the highest antioxidative activity are obtained for the ortho-diphenols hydroxytyrosol, oleuropein, and oleacein. The experimentally determined kinetic isotope effects (KIEs) for hydroxytyrosol, homovanillyl alcohol, and caffeic acid reactions are 16.0, 15.4, and 16.7, respectively. Based on these KIEs, thermodynamic activation parameters, and an intrinsic bond orbital (IBO) analysis along the IRC path calculations, we propose a proton-coupled electron transfer mechanism. The average local ionization energy and electron donor Fukui function obtained for the phenolic compounds show that the most reactive electron-donating sites are associated with π electrons above and below the aromatic ring, in support of the IBO analysis and proposed PCET reaction mechanism. Large KIEs and isotopic values of Arrhenius pre-exponential factor AH/AD determined for the hydroxytyrosol, homovanillyl alcohol, and caffeic acid reactions of 0.6, 1.3, and 0.3, respectively, reveal the involvement of hydrogen tunneling in the process.

Understanding the role of Niobium, Molybdenum and Tungsten in realizing of the transparentn-type SnO2.

Based on the density functional theory, the defective band structures (DBSs), ionization energy and formation energy for Niobium (Nb), Molybdenum (Mo) and Tungsten (W)-doped SnO2are calculated. The DBSs show Nb, Mo and W substituting Sn (labeled as NbSn, MoSnand WSn) could form the localized impurity states which are above the conduction band minimum (CBM). These characteristics can be attributed to the energy of dopants' d-orbitals are much higher than that of Sn-s and -d orbital as well as O-2p orbitals, and the dopants with their neighboring atoms would form the non-bonding impurity states. The DBSs confirm NbSn, MoSnand WSnare typicaln-type defects in SnO2. The ionization energiesϵ(0/+) for NbSn, MoSnand WSnare higher than 0.22 eV above CBM, indicating these defects could be fully ionized. We find the NbO and MoO3are promising dopant sources, as the thermodynamic equilibrium fabrication scheme is considered. Taking Nb-doped SnO2as an example, we find a few NbSncould induce high conductivity (541 S cm-1). These results suggest that SnO2containing NbSn, MoSnand WSnare promisingn-type semiconductors. Our findings would provide a better understanding of then-type properties in Nb, Mo and W-doped SnO2.

Energy-Level Interpretation of Carbazole Derivatives in Self-Assembling Monolayer.

Energy-level alignment is a crucial factor in the performance of thin-film devices, such as organic light-emitting diodes and photovoltaics. One way to adjust these energy levels is through chemical modification of the molecules involved. However, this approach may lead to unintended changes in the optical and/or electrical properties of the compound. An alternative method for energy-level adjustment at the interface is the use of self-assembling monolayers (SAMs). Initially, SAMs with passive spacers were employed, creating a surface dipole moment that altered the work function (WF) of the electrode. However, recent advancements have led to the synthesis of SAM molecules with active spacers. This development necessitates considering not only the modification of the electrode's WF but also the ionization energy (IE) of the molecule itself. To measure both the IE of SAM molecules and their impact on the electrode's WF, a relatively simple method is photo-electric emission spectroscopy. Solar cell performance parameters have a higher correlation coefficient with the ionization energy of SAM molecules with carbazole derivatives as spacers (up to 0.97) than the work function of the modified electrode (up to 0.88). Consequently, SAMs consisting of molecules with active spacers can be viewed as hole transport layers rather than interface layers.

Superalkalis with Hydrogen as Central Electronegative Atom and their Possible Applications: Ab Initio and DFT Study.

Superalkalis are unusual species having ionization energies lower than that of the alkali metals. These species with various applications are of great importance in chemistry due to their low ionization energies and strong reducing property. A typical superalkali contains a central electronegative core decorated with excess metal ligands. In the quest for novel superalkalis, we have designed the superalkalis HLi2, HLiNa and HNa2 using hydrogen as central electronegative atom for the first time employing high level ab initio (CCSD(T), MP2) and density functional theory (ωB97X-D) methods. The superalkalis exhibit very low ionization energies, even lower than that of cesium. Stability of these species is verified from binding energy and dissociation energy values. The superalkalis are capable of reducing SO2, NO, CO2, CO and N2 molecules by forming stable ionic complexes and therefore can be used as catalysts for the reduction or activation of systems possessing very low electron affinities. The superalkalis form stable supersalts with tailored properties when interact with a superhalogen. They also show remarkably high non-linear optical responses, hence could have industrial applications. It is hoped that this work will enrich the superalkali family and spur further theoretical and experimental research in this direction.

Limiting factors in the accuracy of DFT calculation for redox potentials.

In the present study, we have investigated factors affecting the accuracy of computational chemistry calculation of redox potentials, namely the gas-phase ionization energy (IE) and electron affinity (EA), and the continuum solvation effect. In general, double-hybrid density functional theory methods yield IEs and EAs that are on average within ~0.1 eV of our high-level W3X-L benchmark, with the best performing method being DSD-BLYP/ma-def2-QZVPP. For lower-cost methods, the average errors are ~0.2-0.3 eV, with ωB97X-3c being the most accurate (~0.15 eV). For the solvation component, essentially all methods have an average error of ~0.3 eV, which shows the limitation of the continuum solvation model. Curiously, the directly calculated redox potentials show errors of ~0.3 eV for all methods. These errors are notably smaller than what can be expected from error propagation with the two components (IE and EA, and solvation effect). Such a discrepancy can be attributed to the cancellation of errors, with the lowest-cost GFN2-xTB method benefiting the most, and the most accurate ωB97X-3c method benefiting the least. For organometallic species, the redox potentials show large deviations exceeding ~0.5 eV even for DSD-BLYP. The large errors are attributed to those for the gas-phase IEs and EAs, which represents a major barrier to the accurate calculation of redox potentials for such systems.

Direct Experimental Observation of the Tetrabromine Cluster Br4 by Synchrotron Photoionization Mass Spectrometry.

We present a first spectroscopic characterization of the homoatomic polyhalogen tetrabromine, Br4, in the gas phase. Photolysis of CHBr3 at 248 nm is used to generate atomic bromine radicals in a flow tube reactor. Resulting combination products are detected by photoionization mass spectrometry at the Advanced Light Source of the Lawrence Berkeley National Laboratory. Interpretation of the experimental mass spectra is informed by calculated adiabatic ionization energies carried out at the CCSD(T)/aug-cc-pVTZ//M06-2X/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ//cam-B3LYP/6-311++g** levels of theory. Tunable VUV synchrotron radiation enables the collection of the mass-selected photoionization spectra by which Br4 is assigned using Franck-Condon simulations of a Br2 dimer with a stretched tetrahedral geometry.

Absolute Photoionization Cross Section and Dissociative Ionization Pathways of Alpha-Pinene.

The absolute photoionization cross section of the monoterpenoid, alpha-pinene (AP), is presented together with the relative photoionization cross sections of its dissociative fragments for the first time. Experiments are performed via multiplexed vacuum ultraviolet (VUV) synchrotron photoionization (PI) mass spectrometry in the 8.0-11.0 eV energy range. Experimental work is conducted at the Advanced Light Source of the Lawrence Berkeley National Laboratory. Dissociative fragments were identified at m/z 121, 94, 93, 92, and 80. The photoionization cross section for the parent mass at 11.0 eV was determined to be 17±4 Mb with a total ionization cross section of 92±23 Mb at the same photon energy. Experimental appearance energies of dissociative ionization fragments and potential dissociative ionization pathways calculated at the G4 level of theory are presented as well.

The verification of delta SCF and Slater's transition state theory for the calculation of core ionization energy.

The core ionization energies of second- and third-period elements of the molecules C2 H5 NO2 , SiF4 , Si(CH3 )4 , PF3 , POF3 , PSF3 , CS2 , OCS, SO2 , SO2 F2 , CH3 Cl, CFCl3 , SF5 Cl, and Cl3 PS are calculated by using Hartree-Fock (HF), and Kohn-Sham (KS) with BH&HLYP, B3LYP, and LC-BOP functionals. We used ΔSCF, Slater's transition state (STS), and two previously proposed shifted STS (1) and shifted STS (2) methods, which have been developed. The errors of ΔSCF and STS come mainly from the self-interaction errors (SIE) and can be corrected with a shifting scheme. In this study, we used the shifting parameters determined for each atom. The shifted STS (1) reproduces ΔSCF almost perfectly with mean absolute deviations (MAD) of 0.02 eV. While ΔSCF and STS vary significantly depending on the functional used, the variation of shifted STS (2) is small, and all shifted STS (2) values are close to the observed ones. The deviations of the shifted STS (2) from the experiment are 0.24 eV (BH&HLYP), 0.19 eV (B3LYP), and 0.23 eV (LC-BOP). These results further support the use of shifted STS methods for predicting the core ionization energies.

Unraveling the Impact of Acetylation Patterns in Chitosan Oligomers on Cu2+ Ion Binding: Insights from DFT Calculations.

Chitosans are partially acetylated polymers of glucosamine, structurally characterized by their degree of polymerization as well as their fraction and pattern of acetylation. These parameters strongly influence the physico-chemical properties and biological activities of chitosans, but structure-function relationships are only poorly understood. As an example, we here investigated the influence of acetylation on chitosan-copper complexation using density functional theory. We investigated the electronic structures of completely deacetylated and partially acetylated chitosan oligomers and their copper-bound complexes. Frontier molecular orbital theory revealed bonding orbitals for electrophiles and antibonding orbitals for nucleophiles in fully deacetylated glucosamine oligomers, while partially acetylated oligomers displayed bonding orbitals for both electrophiles and nucleophiles. Our calculations showed that the presence of an acetylated subunit in a chitosan oligomer affects the structural and the electronic properties of the oligomer by generating new intramolecular interactions with the free amino group of neighboring deacetylated subunits, thereby influencing its polarity. Furthermore, the band gap energy calculated from the fully and partially deacetylated oligomers indicates that the mobility of electrons in partially acetylated chitosan oligomers is higher than in fully deacetylated oligomers. In addition, fully deacetylated oligomers form more stable complexes with higher bond dissociation energies with copper than partially acetylated ones. Interestingly, in partially acetylated oligomers, the strength of copper binding was found to be dependent on the pattern of acetylation. Our study provides first insight into the influence of patterns of acetylation on the electronic and ion binding properties of chitosans. Depending on the intended application, the obtained results can serve as a guide for the selection of the optimal chitosan for a specific purpose.

Building a new reasonable atomic theory.

CONTEXT: This article is an initiation to build reasonable atomic/molecular theory to study chemicals utilized in different sectors of science including chemistry, biology, and medicine as well as the material science. It is all about opening new pathways and method-developments which need to be simple, reasonable, rational, and applicable to all chemicals and be closely consistent with the experimental data and real world. Hence, the success may simplify the process and eliminate the need to sophisticated software and heavy computations. The article first reviews the current classical atomic theory, and discusses some of its flaws. Then, it suggests a more reasonable approach through several presented simple formulas which would generate results consistent with the experimental data. Finally, the article goes through some examples, cases, and details to present the differences between the new suggested approach and the current classical atomic theory. Building new pathways would help not only with the ongoing scientific achievements but it would also help in classrooms and the education of next future generations. METHODS: All of the calculations and figures presented in this article are done by simple calculators and the use of Microsoft software including excel spreadsheet. The presented atomic theory does not need any sophisticated software and/or heavy computations. If desired, one can also use a simple personal programing technique to generate the desired results. So the key is in better understanding of the subjects and not in development of complicated computational tools and theoretical techniques. This article did not use any of the usual ab initio or DFT, or basis sets, or force field molecular-dynamics techniques. The focus of this article is mainly atomic theory which will expand to molecular theory in future articles.

N-oxidation Regioselectivity and Risk Prediction Using DFT-ALIE Calculations.

INTRODUCTION: The formation of N-oxide degradants is a major concern in development of new drugs due to potential effects on a compound's pharmacological activity. Such effects include but are not limited to solubility, stability, toxicity, and efficacy. In addition, these chemical transformations can impact physicochemical properties that affect drug manufacturability. Hence identification and control of N-oxide transformations is of critical importance in the development of new therapeutics. OBJECTIVE: This study describes the development of an in-silico approach to identify N-oxide formation in APIs with respect to autoxidation. METHODS: Average Local Ionization Energy (ALIE) calculations were carried out using molecular modeling techniques and application of Density Functional Theory (DFT) at the B3LYP/6-31G(d,p) level of theory. A total of 257 nitrogen atoms and 15 different oxidizable nitrogen types were used in developing this method. RESULTS: The results show that ALIE could be reliably used to predict the most susceptible nitrogen for N-oxide formation. A risk scale was developed that rapidly categorizes nitrogen's oxidative vulnerabilities as small, medium, or high. CONCLUSIONS: The developed process presents a powerful tool to identify structural susceptibilities for N-oxidation as well as enabling rapid structure elucidation in resolving potential experimental ambiguities.

The radiation response measurement of a single and multiple cell ionization of neuroblastoma cells by infrared laser trap.

Neuroblastoma (NB) is a common type of cancer found mostly in infants and arising from the immature neural crest cells of the sympathetic nervous system. Using laser trapping (LT) technique, the present work contributes to advancing radiotherapy (RT), a leading treatment method for cancer. A single, 2-cells, 3-cells, 4-cells, and 5-cells were trapped using the high-intensity gradient infrared laser at 1064 nm and allowed to become ionized. In this work, a systematic study of Threshold Ionization Energy (TIE) and Threshold Radiation Dose (TRD) versus mass for both single and multi-cell ionization using laser trapping (LT) techniques on NB is presented. The results show that TIE increased as the mass of cells increased, meanwhile TRD decreased with the increase of cell mass. We observed an inverse correlation between TRD and cell mass. We demonstrate how to compute the maximum radiation dosage for cell death using the LT technique. Results show a possible blueprint for computing the TRD in vivo. The use of multiple cell ionization to determine radiation dosage along with better data accuracy concerning the tumor size and density will have profound implications for radiation dosimetry. The diminution in TRD becomes more significant in multiple cell ionization as we see in TRD vs the number of cells entering the trap. This is due to the chain effect generated by radiation and the absorption by water molecules at 1064 nm. This result provides us with better insight into the optimization of the therapeutic ratio.

Ionization of Decamethylmanganocene: Insights from the DFT-Assisted Laser Spectroscopy.

Metallocenes represent one of the most important classes of organometallics with wide prospects for practical use in various fields of chemistry, materials science, molecular electronics, and biomedicine. Many applications of these metal complexes are based on their ability to form molecular ions. We report the first results concerning the changes in the molecular and electronic structure of decamethylmanganocene, Cp*2Mn, upon ionization provided by the high-resolution mass-analyzed threshold ionization (MATI) spectroscopy supported by DFT calculations. The precise ionization energy of Cp*2Mn is determined as 5.349 ± 0.001 eV. The DFT modeling of the MATI spectrum shows that the main structural deformations accompanying the detachment of an electron consist in the elongation of the Mn-C bonds and a change in the Me out-of-plane bending angles. Surprisingly, the DFT calculations predict that most of the reduction in electron density (ED) upon ionization is associated with the hydrogen atoms of the substituents, despite the metal character of the ionized orbital. However, the ED difference isosurfaces reveal a complex mechanism of the charge redistribution involving also the carbon atoms of the molecule.

Atomic excited states and the related energy levels.

This article is about generalization and extension of the Bohr atomic model as well as the Rydberg formula to make them applicable to all atomic/ionic excited states and their energy levels. Bohr and Rydberg's original works were deemed only for hydrogen and the hydrogen-like ions but in time many mistakenly have come to the conclusion that those original forms of the theory are applicable to all species. This article clarifies the subject and helps with the misunderstandings. The article reviews first the original theory of atoms, the related excited states, and the related energy levels. It then shows the shortcoming of the original formulations and makes changes to generalize the theory and extend their applications to all atoms and their related ions. The theory of atomic excited states is re-formulated using a newly defined parameter called "characteristic exponent k" and the corresponding ionization energy. Numerical calculations and detailed works for several elements are presented to establish a better understanding of excited states. The article seeks also for a connection between the atomic energy levels and the internal structures and inner electrons of atoms. Furthermore, a small data bank is generated using the calculated "characteristic exponents k" for elements to be utilized for future simulations, studies, and research activities.

The Energy Level Conundrum of Organic Semiconductors in Solar Cells.

The frontier molecular energy levels of organic semiconductors are decisive for their fundamental function and efficiency in optoelectronics. However, the precise determination of these energy levels and their variation when using different techniques makes it hard to compare and establish design rules. In this work, the energy levels of 33 organic semiconductors via cyclic voltammetry (CV), density functional theory, ultraviolet photoelectron spectroscopy, and low-energy inverse photoelectron spectroscopy are determined. Solar cells are fabricated to obtain key device parameters and relate them to the significant differences in the energy levels and offsets obtained from different methods. In contrast to CV, the photovoltaic gap measured using photoelectron spectroscopy (PES) correlates well with the experimental device VOC . It is demonstrated that high-performing systems such as PM6:Y6 and WF3F:Y6, which are previously reported to have negligible ionization energy (IE) offsets (ΔIE), possess sizable ΔIE of ≈0.5 eV, determined by PES. Using various D-A blends, it is demonstrated that ΔIE plays a key role in charge generation. In contrast to earlier reports, it is shown that a vanishing ΔIE is detrimental to device performance. Overall, these findings establish a solid base for reliably evaluating material energetics and interpreting property-performance relationships in organic solar cells.

The second derivative of the electronic energy with respect to the compression scaling factor in the XP-PCM model: Theory and applications to compression response functions of atoms.

We present the analytical theory for the second derivative of the electronic energy with respect to the scaling factor of the compression cavity within the eXtreme pressure polarizable continuum model (XP-PCM) for the study of compressed atomic and molecular systems. The theory has been exploited to study compression response functions describing how the atomic/molecular properties are effected by an external pressure. The response functions considered include the atomic compressibility and the pressure coefficients of the ionization energy (IE) and electron affinity (EA). The theory has been validated by numerical application to compressed neon, argon, and krypton atoms.

Update of Atomic Data for the First Three Spectra of Actinium.

The present article describes a complete reanalysis of all published data on observed spectral lines and energy levels of the first three spectra of actinium (Ac I-III). In Ac I, three previously determined energy levels have been rejected, 12 new energy levels have been found; for six previously known levels, either the J values or the energies have been revised, and the ionization energy has been redetermined with an improved accuracy. In the line list of Ac I, three previous classifications have been discarded, 16 new ones have been found, and three have been revised. In Ac II, 16 new energy levels have been established, and 36 new identifications have been found for previously observed but unclassified lines. In both Ac I and Ac II, new sets of transition probabilities have been calculated. For all three spectra, complete datasets of critically evaluated energy levels, observed lines, and transition probabilities have been constructed to serve as recommended data on these spectra.

CO2 Activation Within a Superalkali-Doped Fullerene.

With the aim of finding a suitable synthesizable superalkali species, using the B3LYP/6-31G* density functional level of theory we provide results for the interaction between the buckminsterfullerene C60 and the superalkali Li3F2. We show that this endofullerene is stable and provides a closed environment in which the superalkali can exist and interact with CO2. It is worthwhile to mention that the optimized Li3F2 structure inside C60 is not the most stable C2v isomer found for the "free" superalkali but the D3h geometry. The binding energy at 0 K between C60 and Li3F2 (D3h) is computed to be 119 kJ mol-1. Once CO2 is introduced in the endofullerene, it is activated, and the O C O ^ angle is bent to 132°. This activation does not follow the previously studied CO2 reduction by an electron transfer process from the superalkali, but it is rather an actual reaction where a F (from Li3F2) atom is bonded to the CO2. From a thermodynamic analysis, both CO2 and the encapsulated [Li3F2⋅CO2] are destabilized in C60 with solvation energies at 0 K of 147 and < -965 kJ mol-1, respectively.

The Schottky-Mott Rule Expanded for Two-Dimensional Semiconductors: Influence of Substrate Dielectric Screening.

A comprehensive understanding of the energy level alignment mechanisms between two-dimensional (2D) semiconductors and electrodes is currently lacking, but it is a prerequisite for tailoring the interface electronic properties to the requirements of device applications. Here, we use angle-resolved direct and inverse photoelectron spectroscopy to unravel the key factors that determine the level alignment at interfaces between a monolayer of the prototypical 2D semiconductor MoS2 and conductor, semiconductor, and insulator substrates. For substrate work function (Φsub) values below 4.5 eV we find that Fermi level pinning occurs, involving electron transfer to native MoS2 gap states below the conduction band. For Φsub above 4.5 eV, vacuum level alignment prevails but the charge injection barriers do not strictly follow the changes of Φsub as expected from the Schottky-Mott rule. Notably, even the trends of the injection barriers for holes and electrons are different. This is caused by the band gap renormalization of monolayer MoS2 by dielectric screening, which depends on the dielectric constant (εr) of the substrate. Based on these observations, we introduce an expanded Schottky-Mott rule that accounts for band gap renormalization by εr -dependent screening and show that it can accurately predict charge injection barriers for monolayer MoS2. It is proposed that the formalism of the expanded Schottky-Mott rule should be universally applicable for 2D semiconductors, provided that material-specific experimental benchmark data are available.

From Electronegativity towards Reactivity-Searching for a Measure of Atomic Reactivity.

Pauling introduced the concept of electronegativity of an atom which has played an important role in understanding the polarity and ionic character of bonds between atoms. We set out to define a related concept of atomic reactivity in such a way that it can be quantified and used to predict the stability of covalent bonds in molecules. Guided by the early definition of electronegativity by Mulliken in terms of first ionization energies and Pauling in terms of bond energies, we propose corresponding definitions of atomic reactivity. The main goal of clearly distinguishing the inert gas atoms as nonreactive is fulfilled by three different proposed measures of atomic reactivity. The measure likely to be found most useful is based on the bond energies in atomic hydrides, which are related to atomic reactivities by a geometric average. The origin of the atomic reactivity is found in the symmetry of the atomic environment and related conservation laws which are also the origin of the shell structure of atoms and the periodic table. The reactive atoms are characterized by degenerate or nearly degenerate (several states of the same or nearly the same energy) ground states, while the inert atoms have nondegenerate ground states and no near-degeneracies. We show how to extend the use of the Aufbau model of atomic structure to qualitatively describe atomic reactivity in terms of ground state degeneracy. The symmetry and related conservation laws of atomic electron structures produce a strain (energy increase) in the structure, which we estimate by use of the Thomas-Fermi form of DFT implemented approximately with and without the symmetry and conservation constraints. This simplified and approximate analysis indicates that the total strain energy of an atom correlates strongly with the corresponding atomic reactivity measures but antibonding mechanisms prevent full conversion of strain relaxation to bonding.