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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Antiradical Properties of trans-2-(4-substituted-styryl)-thiophene.

2-substituted thiophene compounds with electron donating and electron withdrawing p-phenyl substitution were synthesized and studied their radical scavenging properties using DPPH assay and DFT method. It is shown that p-hydroxy and p-amino phenyl substituted compound exhibit radical scavenging activity. From DFT and radical scavenging studies, a correlation between IC50 with the bond dissociation enthalpy, proton affinity, ground state dipole moment and optical band gap of compound is found. Compounds 1-3 with electron withdrawing substituent (NO2, CN, Cl) do not show any radical scavenging properties, whereas compounds 6-7 with electron donating substituent (OH, NH2) show antiradical properties. Further, the antiradical activity is reduced drastically by replacing the -OH and -NH2 with methoxy and -N-alkylating group respectively in 6 and 7. The compound with p-hydroxy phenyl substitution, exhibits stronger antiradical activity as compared to the p-amino phenyl substitution due to smaller O-H bond dissociation energy as compared to the N-H bond. From DPPH and DFT studies, it is suggested that the radical scavenging activity in 2-substituted thiophene is occurred through proton transfer mechanism. The other possible SET, SPLET mechanisms are also corroborated. Graphical Abstract Antiradical properties of trans-2-(4-substituted-styryl)-thiophene Anamika Gusain, Naresh Kumar, Jagdeep Kumar, Gunjan Pandey, Prasanta Kumar Hota.

Exploring extra dimensions to capture saliva metabolite fingerprints from metabolically healthy and unhealthy obese patients by comprehensive two-dimensional gas chromatography featuring Tandem Ionization mass spectrometry.

This study examines the information potential of comprehensive two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GC×GC-TOF MS) and variable ionization energy (i.e., Tandem Ionization™) to study changes in saliva metabolic signatures from a small group of obese individuals. The study presents a proof of concept for an effective exploitation of the complementary nature of tandem ionization data. Samples are taken from two sub-populations of severely obese (BMI > 40 kg/m2) patients, named metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO). Untargeted fingerprinting, based on pattern recognition by template matching, is applied on single data streams and on fused data, obtained by combining raw signals from the two ionization energies (12 and 70 eV). Results indicate that at lower energy (i.e., 12 eV), the total signal intensity is one order of magnitude lower compared to the reference signal at 70 eV, but the ranges of variations for 2D peak responses is larger, extending the dynamic range. Fused data combine benefits from 70 eV and 12 eV resulting in more comprehensive coverage by sample fingerprints. Multivariate statistics, principal component analysis (PCA), and partial least squares discriminant analysis (PLS-DA) show quite good patient clustering, with total explained variance by the first two principal components (PCs) that increases from 54% at 70 eV to 59% at 12 eV and up to 71% for fused data. With PLS-DA, discriminant components are highlighted and putatively identified by comparing retention data and 70 eV spectral signatures. Within the most informative analytes, lactose is present in higher relative amount in saliva from MHO patients, whereas N-acetyl-D-glucosamine, urea, glucuronic acid γ-lactone, 2-deoxyribose, N-acetylneuraminic acid methyl ester, and 5-aminovaleric acid are more abundant in MUO patients. Visual feature fingerprinting is combined with pattern recognition algorithms to highlight metabolite variations between composite per-class images obtained by combining raw data from individuals belonging to different classes, i.e., MUO vs. MHO.Graphical abstract.

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.

Constraint structure optimization to a specific minimum using ionization energy.

A structure optimization method with ionization energy constraint is developed to explore structures with specific ionization energy. The Levine-Coe-Martínez penalty function (J Phys Chem B 2008, 112, 405) was adopted, and the penalty function includes a predefined core-ionization energy and inner-shell ionization energy. For an SN 2 reaction, isomerization of a platinum complex, a proton transfer reaction, and carbon monoxide adsorption on a palladium cluster, the present method was tested, and the targeted energy minima were obtained as designated by the input ionization energy. The shape of the objective function, the parameters in the penalty function, and structural changes during the optimization process were discussed. An automated parameter setting and possible problems are discussed for future direction. © 2018 Wiley Periodicals, Inc.

Recent Progress on the Design, Characterization, and Application of Superalkalis.

Superalkalis are clusters or molecules featuring lower ionization energies (IEs) than that of cesium atoms, and thus exhibit excellent reducing properties. Such special species have great potential to be used in the synthesis of unusual charge-transfer salts and cluster-assembled nanomaterials with tailored properties, in the reduction of carbon dioxide, or as hydrogen storage materials and noble-gas-trapping agents, etc. In this regard, ongoing efforts have been devoted to designing and characterizing superalkalis of new types. The recent progress on the study of superalkalis in terms of theoretical design, characterization, and potential application is summarized in this minireview. We hope this review will not only provide a broad overview of this research field, but also highlight the prospect of further extending the experimental synthesis and practical application of superalkalis.

Decomposition of Picolyl Radicals at High Temperature: A Mass Selective Threshold Photoelectron Spectroscopy Study.

The reaction products of the picolyl radicals at high temperature were characterized by mass-selective threshold photoelectron spectroscopy in the gas phase. Aminomethylpyridines were pyrolyzed to initially produce picolyl radicals (m/z=92). At higher temperatures further thermal reaction products are generated in the pyrolysis reactor. All compounds were identified by mass-selected threshold photoelectron spectroscopy and several hitherto unexplored reactive molecules were characterized. The mechanism for several dissociation pathways was outlined in computations. The spectrum of m/z=91, resulting from hydrogen loss of picolyl, shows four isomers, two ethynyl pyrroles with adiabatic ionization energies (IEad ) of 7.99 eV (2-ethynyl-1H-pyrrole) and 8.12 eV (3-ethynyl-1H-pyrrole), and two cyclopentadiene carbonitriles with IE's of 9.14 eV (cyclopenta-1,3-diene-1-carbonitrile) and 9.25 eV (cyclopenta-1,4-diene-1-carbonitrile). A second consecutive hydrogen loss forms the cyanocyclopentadienyl radical with IE's of 9.07 eV (T0 ) and 9.21 eV (S1 ). This compound dissociates further to acetylene and the cyanopropynyl radical (IE=9.35 eV). Furthermore, the cyclopentadienyl radical, penta-1,3-diyne, cyclopentadiene and propargyl were identified in the spectra. Computations indicate that dissociation of picolyl proceeds initially via a resonance-stabilized seven-membered ring.

Detailed analysis of the vibronic structure of phenetole in its first excited state and ionic ground state.

The vibronic structure of the first electronically excited state S1 and ionic ground state D0 of phenetole has been investigated by means of resonance enhanced multi photon ionization (REMPI) and mass analyzed threshold ionization (MATI) spectroscopy. The vibronic levels were assigned with the aid of quantum chemical calculations at the (TD)DFT level of theory and a multidimensional Franck-Condon approach. The S1 excitation energy of phenetole has been determined to be 36370 ± 4 cm-1 (4.5093 ± 0.0005 eV). The adiabatic ionization energy was determined to be 65665 ± 7 cm-1 (8.1415 ± 0.0008 eV). The vibronic structure has been analyzed whereby the in-plane bending vibration νbend shows high activity in the first excited state but is more pronounced in the ionic ground state. Moreover, a strong Duschinsky rotation effect can be observed for several D0←S1 transitions that causes violations of the Δv = 0 propensity rule.

Accurate Ionization Energies for Mononuclear Copper Complexes Remain a Challenge for Density Functional Theory.

Copper is ubiquitous and its one-electron redox chemistry is central to many catalytic processes. Modeling such chemistry requires electronic structure methods capable of the accurate prediction of ionization energies (IEs) for compounds including copper in different oxidation states and supported by various ligands. Herein, we estimate IEs for 12 mononuclear Cu species previously reported in the literature by using 21 modern density functionals and the DLPNO-CCSD(T) wave function theory model; we consider extrapolated values of the latter to provide reference values of acceptable accuracy. Our results reveal a considerable diversity in functional performance. Although there is nearly always at least one functional that performs well for any given species, there are none that do so for every member of the test set, and certain cases are particularly pathological. Over the entire test set, the SOGGA11-X functional performs best with a mean unsigned error (MUE) of 0.22 eV. PBE0, ωB97X-D, CAM-B3LYP, M11-L, B3LYP, and M11 exhibit MUEs ranging between 0.23 and 0.34 eV. When including relativistic effects with the zero-order regular approximation, ωB97X-D, CAM-B3LYP, and PBE0 are found to provide the best accuracy.

Scrutinizing Defects and Defect Density of Selenium-Doped Graphene for High-Efficiency Triiodide Reduction in Dye-Sensitized Solar Cells.

Understanding the impact of the defects/defect density of electrocatalysts on the activity in the triiodide (I3- ) reduction reaction of dye-sensitized solar cells (DSSCs) is indispensable for the design and construction of high-efficiency counter electrodes (CEs). Active-site-enriched selenium-doped graphene (SeG) was crafted by ball-milling followed by high-temperature annealing to yield abundant edge sites and fully activated basal planes. The density of defects within SeG can be tuned by adjusting the annealing temperature. The sample synthesized at an annealing temperature of 900 °C exhibited a superior response to the I3- reduction with a high conversion efficiency of 8.42 %, outperforming the Pt reference (7.88 %). Improved stability is also observed. DFT calculations showed the high catalytic activity of SeG over pure graphene is a result of the reduced ionization energy owing to incorporation of Se species, facilitating electron transfer at the electrode-electrolyte interface.

Deionization of Dopants in Silicon Nanofilms Even with Donor Concentration of Greater than 10(19) cm(-3).

Understanding the dopant properties in heavily doped nanoscale semiconductors is essential to design nanoscale devices. We report the deionization or finite ionization energy of dopants in silicon (Si) nanofilms with dopant concentration (ND) of greater than 10(19) cm(-3), which is in contrast to the zero ionization energy (ED) in bulk Si at the same ND. From the comparison of experimentally observed and theoretically calculated ED, we attribute the deionization to the suppression of metal-insulator transition in highly doped nanoscale semiconductors in addition to the quantum confinement and the dielectric mismatch, which greatly increase ED in low-doped nanoscale semiconductors. Thus, for nanoscale transistors, ND should be higher than that estimated from bulk Si dopant properties in order to reduce their resistivity by the metal-insulator transition.