Revision of the Thermodynamics of the Proton in Gas Phase

Antioxidant activity of an inclusion complex between rutin and β-cyclodextrin: experimental and quantum chemical studies

This study aims to synthesize a guest-host complex derived from rutin (Rut) and β-cyclodextrin (β-CD) (denoted as [Rut⊂β-CD]). The obtained substance was characterized by the FT-IR and DSC methods, signifying the formation of an inclusion complex between Rut and β-CD. Complex formation increased the antioxidant activity of rutin corresponding to the decrease of EC50 values from 1.547 × 10-5 mol L-1 to 1.227 × 10-5 mol L-1 according to the DPPH free radical scavenging test. The rutin-β-CD interaction energies were calculated in the vacuum and various solvents (e.g., water, ethanol, and dimethylsulfoxide) utilizing an accurate and broadly parametrized self-consistent tight-binding quantum chemical method (GFN2-xTB). The calculation results reveal the influence of solvent on the structural formation of the rutin-β-CD complex. In both the vacuum and aqueous solution, rutin can enter into the small-sized empty cavity of β-CD, albeit through different terminals, resulting in distinct preferential structures. The presence of organic solvents appears to reduce the interaction between rutin and β-CD, with the interaction strength following the order: water > ethanol > dimethyl sulfoxide.

Unlocking the potential of phenolated kraft lignin as a versatile feed additive

Lignin, a renewable natural antioxidant and bacteriostat, holds promise as a versatile, cost-effective feed additive. However, traditional industrial lignin faces limitations, including low reactivity, poor uniformity, and unstable properties, necessitating chemical modification. Complex modification methods pose economic and toxicity challenges, so this study adopted a relatively simple alkali-catalyzed phenolization approach, using phenol, catechol, and pyrogallol to modify kraft lignin, and characterized the resulting products using various techniques. Subsequently, their antioxidant, antibacterial, adsorption properties for heavy metal ions and mycotoxins, growth-promoting properties, and antiviral abilities were assessed. The phenolation process led to lignin depolymerization and a notable increase in phenolic hydroxyl content, particularly in pyrogallol-phenolated lignin (Py-L), rising from 3.08 to 4.68 mmol/g. These modified lignins exhibited enhanced antioxidant activity, with over 99 % inhibition against E. coli and S. aureus, and remarkable adsorption capacities for heavy metal ions and mycotoxins. Importantly, Py-L improved the growth performance of mice and reduced influenza mortality. Furthermore, density functional theory calculations elucidated the mechanism behind the enhanced antioxidant properties. This study presents a promising avenue for developing versatile feed additives to address challenges related to animal feed antioxidant supplementation, bacterial control, and growth promotion.

Strong Bases and beyond: The Prominent Contribution of Neutral Push-Pull Organic Molecules towards Superbases in the Gas Phase

In this review, the principles of gas-phase proton basicity measurements and theoretical calculations are recalled as a reminder of how the basicity PA/GB scale, based on Brønsted-Lowry theory, was constructed in the gas-phase (PA-proton affinity and/or GB-gas-phase basicity in the enthalpy and Gibbs energy scale, respectively). The origins of exceptionally strong gas-phase basicity of some organic nitrogen bases containing N-sp3 (amines), N-sp2 (imines, amidines, guanidines, polyguanides, phosphazenes), and N-sp (nitriles) are rationalized. In particular, the role of push-pull nitrogen bases in the development of the gas-phase basicity in the superbasicity region is emphasized. Some reasons for the difficulties in measurements for poly-functional nitrogen bases are highlighted. Various structural phenomena being in relation with gas-phase acid-base equilibria that should be considered in quantum-chemical calculations of PA/GB parameters are discussed. The preparation methods for strong organic push-pull bases containing a N-sp2 site of protonation are briefly reviewed. Finally, recent trends in research on neutral organic superbases, leaning toward catalytic and other remarkable applications, are underlined.

Characterizing Hydroxyl Radical Formation from the Light-Driven Fe(II)-Peracetic Acid Reaction, a Key Process for Aerosol-Cloud Chemistry

The reaction of peracetic acid (PAA) and Fe(II) has recently gained attention due to its utility in wastewater treatment and its role in cloud chemistry. Aerosol-cloud interactions, partly mediated by aqueous hydroxyl radical (OH) chemistry, represent one of the largest uncertainties in the climate system. Ambiguities remain regarding the sources of OH in the cloud droplets. Our research group recently proposed that the dark and light-driven reaction of Fe(II) with peracids may be a key contributor to OH formation, producing a large burst of OH when aerosol particles take up water as they grow to become cloud droplets, in which reactants are consumed within 2 min. In this work, we quantify the OH production from the reaction of Fe(II) and PAA across a range of physical and chemical conditions. We show a strong dependence of OH formation on ultraviolet (UV) wavelength, with maximum OH formation at λ = 304 ± 5 nm, and demonstrate that the OH burst phenomenon is unique to Fe(II) and peracids. Using kinetics modeling and density functional theory calculations, we suggest the reaction proceeds through the formation of an [Fe(II)-(PAA)2(H2O)2] complex, followed by the formation of a Fe(IV) complex, which can also be photoactivated to produce additional OH. Determining the characteristics of OH production from this reaction advances our knowledge of the sources of OH in cloudwater and provides a framework to optimize this reaction for OH output for wastewater treatment purposes.

Computational-based investigation of antioxidative potential polyphenolic compounds of Salvia officinalis L.: combined DFT and molecular docking approaches

CONTEXT

The antioxidant properties of the three polyphenolic compounds (carnosol, cirsiliol, and luteolin) of Salvia officinalis L. were investigated employing the density functional theory (DFT) calculations at the B3LYP of basis set at 6-311 +  + G (d, p) in order to evaluate their antioxidant activity. The enthalpies of reactions associated with the SET-PT, SPLET, and HAT mechanisms were analyzed in gas and in different solvents using the CPCM (conductor-like polarizable continuum) model. For all possible hydrogen donor sites, the corresponding parameters (BDE, AIP, PDE, PA, ETE, HOMOs, and LUMOs) and reactivity indices (IPE, EA, Χ, η, S, and ω) were also evaluated. The calculated results showed that derivatives 12-OH, 11-OH, 4'-OH, and 3'-OH had the lowest antioxidant activity. The results showed as well that carnosol, cirsiliol, and luteolin have higher reactivity compared to ascorbic acid and could be considered better antioxidants. According to research, the catechol group is crucial in influencing the studied compounds antioxidant activity. The theoretically predicted order of antioxidant efficiencies in this work agrees well with the QSAR (quantitative structure-activity relationship) data. The findings show that in the vacuum as well as benzene media. HAT would be the most effective mechanism; in contrast, the thermodynamic equilibrium approach in polar media is the SPLET mechanism. Likewise, the outcomes of the docking modeling confirm that the selected molecules have high inhibitory activity to glutathione-S-transferases (GSTs) receptors. Moreover, they have very important pharmacokinetic, chemical, and biological profiles. Finally, all the results show that the three natural molecules have good pharmacokinetic profiles, particularly the bioavailability and permeability toward biological membranes.

METHODS

The software packages used in this investigation are Gaussian 16, Discovery studio Visualizer, and AutoDock vina. The three compounds (carnosol, cirsiliol, and luteolin) of Salvia officinalis L. were optimized with DFT/B3LYP of basis set at 6-311 +  + G (d, p). The optimized structures were established via vibrational analysis (i.e., no imaginary frequencies in the frequency set). All enthalpies were zero-point (ZPE) corrected. Vibrational frequency calculations were performed at 298.15 K and 1 atmosphere pressure to determine the thermodynamic characteristics of the investigated reactions. The descriptors were associated with the antioxidant mechanisms for investigated molecules in vacuum and in various solvents. The molecular docking was used by AutoDock vina to estimate and evaluate the title compounds compatibility as potential antioxidant drugs utilizing appropriate receptor proteins. The solvation effect in the medium of benzene (ɛ = 2.27) and water (ɛ = 78.39) was taken into account. Furthermore, a methanol solvent (ɛ = 32.61) was also taken into consideration to compare with the empirical data.

Solvation energies of the ferrous ion in water and in ammonia at various temperatures

CONTEXT

The solvation of metal ions is crucial to understanding relevant properties in physics, chemistry, or biology. Therefore, we present solvation enthalpies and solvation free energies of the ferrous ion in water and ammonia. Our results agree well with the experimental reports for the hydration free energy and hydration enthalpy. We obtained [Formula: see text] kJ mol[Formula: see text] for the hydration free energy and [Formula: see text] kJ mol[Formula: see text] for the hydration enthalpy of ferrous ion in water at room temperature. At ambient temperature, we obtained [Formula: see text] kJ mol[Formula: see text] as the [Formula: see text] ammoniation free energy and [Formula: see text] kJ mol[Formula: see text] for the ammoniation enthalpy. In addition, the free energy of solvation is deeply affected when the temperature increases. This pattern can be attributed to the rise of entropy when the temperature rises. Besides, the temperature does not affect the ammoniation enthalpies and the hydration enthalpy of the [Formula: see text] ion.

METHOD

All the geometry optimizations are performed at the MP2 methods associated with the 6-31++g(d,p) basis set of Pople. solvated phase structures of [Formula: see text] ion in water or in ammonia are performed using the PCM model. The [Formula: see text] program suite was used to perform all the calculations. The program TEMPO was also used to evaluate the temperature sensitivity of the different obtained geometries.

Gas-phase C60Hn+q (n = 0-4, q = 0,1) fullerenes and fulleranes: spectroscopic simulations shed light on cosmic molecular structures

The discovery of C60, C60+, and C70 in the interstellar medium has ignited a profound interest in the astrochemistry of fullerene and related systems. In particular, the presence of diffuse interstellar bands and their association with C60+ has led to the hypothesis that hydrogenated derivatives, known as fulleranes, may also exist in the interstellar medium and contribute to these bands. In this study, we systematically investigated the structural and spectroscopic properties of C60Hn+q (n = 0-4, q = 0,1) using an automated global minimum search and density functional theory calculations. Our results revealed novel global minimum structures for C60H2 and C60H4, distinct from previous reports. Notably, all hydrogenated fullerenes exhibited lower ionization potentials and higher proton affinities compared to C60. From an astrochemical perspective, our results exposed the challenges in establishing definitive spectroscopic criteria for detecting fulleranes using mid-infrared and UV-Vis spectroscopies. However, we successfully identified distinct electronic transitions in the near-infrared range that serve as distinctive signatures of cationic fulleranes. We strongly advocate for further high-resolution experimental studies to fully explore the potential of these transitions for the interstellar detection of fulleranes.

Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models

We present a computational strategy based on thermodynamic cycles to predict and describe the chemical equilibrium between the 3d-transition metal ions Zn²⁺, Cu²⁺, and VO²⁺ and the widely used antineoplastic drug doxorubicin. Our method involves benchmarking a theoretical protocol to compute gas-phase quantities using DLPNO Coupled-Cluster calculations as reference, followed by estimating solvation contributions to the reaction Gibbs free energies using both explicit partial (micro)solvation steps for charged solutes and neutral coordination complexes, as well as a continuum solvation procedure for all solutes involved in the complexation process. We rationalized the stability of these doxorubicin-metal complexes by inspecting quantities obtained from the topology of their electron densities, particularly the bond critical points and non-covalent interaction index. Our approach allowed us to identify representative species in solution phase, infer the most likely complexation process for each case, and identify key intramolecular interactions involved in the stability of these compounds. To the best of our knowledge, this is the first study reporting thermodynamic constants for the complexation of doxorubicin with transition metal ions. Unlike other methods, our procedure is computationally affordable for medium-sized systems and provides valuable insights even with limited experimental data. Furthermore, it can be extended to describe the complexation process between 3d-transition metal ions and other bioactive ligands.

Comparative study of the antioxidant capability of EDTA and Irganox

Oxidative stress makes it difficult to preserve food and negatively affect the applicability of polymeric packaging. It is typically caused by an excess of free radicals, and it is dangerous to human health, resulting in the onset and development of diseases. The antioxidant ability and activity of ethylenediaminetetraacetic acid (EDTA) and Irganox (Irg) as synthetic antioxidant additives were studied. Three different antioxidant mechanisms were considered and compared by calculating bond dissociation enthalpy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE) values. Two density functional theory (DFT) methods were used, M05-2X and M06-2X with the 6-311++G(2d,2p) basis set in gas phase. Both additives can be used to protect pre-processed food products and polymeric packaging from oxidative stress related material deterioration. By comparing the two studied compounds, it was found that EDTA has a higher antioxidant potential than Irganox. To the best of our knowledge several studies have been carried out to understand the antioxidant potential of various natural and synthetic species, but EDTA and Irganox were not compared and investigated before. These additives can be used to protect pre-processed food products and polymeric packaging and prevent material deterioration caused by oxidative stress.

Predicted Negative Ion Photoelectron Spectra of 1-, 2-, and 9-Cyanoanthracene Radical Anions and Computed Thermochemical Values of the Three Cyanoanthracene Isomers

In this work, the negative ion photoelectron spectra of 1-, 2-, and 9-cyanoanthracene (anthracenecarbonitrile, ACN) radical anions, obtained via the calculation of Franck-Condon (FC) factors based on a harmonic oscillator model, are reported. The FC calculations utilize harmonic vibrational frequencies and normal mode vectors derived from density functional theory using the B3LYP/6-311++G (2d,2p) basis set. The removal of an electron from the doublet anion allows for the computation of the negative ion photoelectron spectra that represents the neutral ground singlet state (S_o) and the lowest triplet state (T₁) in each of the three ACN molecules. The respective adiabatic electron affinity (EA) values for the S_o state in 1-, 2-, and 9-ACN isomers are calculated to be 1.353, 1.360, and 1.423 eV. The calculated EA of the 9-cyanoanthracene singlet isomer is in close agreement with the previously reported experimental value of 1.27 ± 0.1 eV. Calculations show that the T₁ states in 1-, 2-, and 9-ACN are located 1.656, 1.663, and 1.599 eV above the S_o state. The calculated T₁ negative ion spectra exhibit intense vibrational origins and weak FC activity beyond the origins, indicating little change in geometry following electron detachment from the doublet anionic state. Upon deprotonation, the EA values of the radical isomers increase by ∼400-700 meV, resulting in neutral deprotonated radicals with EAs between 1.740 and 2.220 eV. The calculated site-specific gas-phase acidity values of ACN isomers indicate that ACN molecules are more acidic than benzonitrile.

From Benzonitrile to Dicyanobenzenes: The Effect of an Additional CN Group on the Thermochemistry and Negative Ion Photoelectron Spectra of Dicyanobenzene Radical Anions

The negative ion photoelectron spectra of 1,2-dicyanobenzene (o-DCNB), 1,3-dicyanobenzene (m-DCNB), and 1,4-dicyanobenzene (p-DCNB) radical anions (DCNB·^-), acquired through the computation of Frack-Condon (FC) factors, are presented. The FC calculations utilize harmonic frequencies and normal mode vectors derived from density functional theory at the B3LYP/aug-cc-pVQZ basis set. All the totally symmetric vibrational modes are treated with Duschinsky rotations to yield neutral DCNBs in their singlet (S_o) and lowest triplet (T₁) states, following an electron removal from the doublet anionic ground state. For the S_o state, the adiabatic electron affinities (EAs) for o-, m-, and p-DCNB are 1.179, 1.103, and 1.348 eV. The EAs for the lowest T₁ state in o-, m-, and p-DCNB are 4.151, 4.185, and 4.208 eV, resulting in an S_o-T₁ energy difference (ΔE_ST) of 2.973, 3.082, and 2.860 eV. A vibrational analysis reveals evidence of FC activity involving ring distortion, C-N bending, and ring C═C stretching vibrational progressions in both the S_o and T₁ states. With the detection of cyanonaphthalene (C₁₀H₇CN) and cyanoindene (C₉H₇CN) in the interstellar medium (ISM), our results highlight the extent to which replacing a single hydrogen on an aromatic molecule with a cyano group, C≡N, can alter the vibrational structure of the molecule/radical anion. As such, dicyano-polyaromatic hydrocarbons may be reasonably robust in the ISM, making it appealing to search for them in future interstellar detection missions.

Guaiacol oxidation: theoretical insight into thermochemistry of radical processes involving methoxy group demethylation

Guaiacol (2-methoxyphenol) is naturally occurring phenolic compound essential in various research areas. Oxidative transformation of guaiacol can lead to the formation of various products, including 1,3-benzodioxole or ortho-quinone. Therefore, this study is focused on the investigation of the reaction enthalpies of experimentally observed guaiacol oxidation pathways in gas-phase, as well as in non-polar environment and aqueous solution. Corresponding Density Functional Theory (DFT) calculations were carried out using two hybrid functionals (M06-2X and B3LYP-D3). All reaction enthalpies, as well as Gibbs free energies, were also calculated using composite ab initio G4 method. M06-2X and G4 results show mutual agreement and the best accordance with available experimentally determined reaction enthalpies. Obtained Gibbs free reaction energies indicate that formation of ortho-quinone is thermodynamically preferred to formation of 1,3-benzodioxole at 298 K in studied environments. Moreover, all computational methods confirm that the reaction enthalpy of methoxy group demethylation, i.e. O-C bond dissociation enthalpy (BDE), is substantially lower in comparison to the enthalpy of hydrogen atom transfer from phenolic OH group. In the case of phenoxide anion of guaiacol, which can be formed in ionization supporting solvents, O-C BDE shows further significant decrease, exceeding 50 kJ mol^-1, in comparison to parent molecule.HIGHLIGHTSReaction enthalpies and Gibbs free energies of individual steps of guaiacol transformation to 1,3-benzodioxole or ortho-quinone are studied in three environments.M06-2X functional and composite ab initio G4 methods provide reliable O-H and O-C bond dissociation enthalpies.Dissociation enthalpy of methoxy group O-C bond is lower by ca. 100 kJ mol^-1 in comparison to phenolic O-H bond.Phenoxide anion of guaiacol shows substantially lower O-C BDE than parent molecule.

Antioxidant Potential of Santowhite as Synthetic and Ascorbic Acid as Natural Polymer Additives

A wide variety of additives are used to improve specific characteristics of the final polymeric product. Antioxidant additives (AAs) can prevent oxidative stress and thus the damage of polymeric materials. In this work, the antioxidant potential and thus the applicability of Santowhite (SW) as synthetic and ascorbic acid (Asc) as natural AAs were explored by using computational tools. Two density functional theory (DFT) methods, M05-2X and M06-2X, have been applied in combination with the 6-311++G(2d,2p) basis set in gas phase. Three antioxidant mechanisms have been considered: hydrogen atom transfer (HAT), single electron transfer-proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET). Bond dissociation enthalpy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE) have been computed for each potential hydrogen donor site. The results indicate that the antioxidant potential of Asc is higher than SW. Furthermore, some of the C-H bonds, depending on their position in the structures, are potent radical scavengers, but O-H groups are more prone to donate H-atoms to free radicals. Nonetheless, both additives can be potentially applied to safeguard common polymers and prohibit oxidative stress-induced material deterioration.

Why Ortho- and Para-Hydroxy Metabolites Can Scavenge Free Radicals That the Parent Atorvastatin Cannot? Important Pharmacologic Insight from Quantum Chemistry

The pharmaceutical success of atorvastatin (ATV), a widely employed drug against the "bad" cholesterol (LDL) and cardiovascular diseases, traces back to its ability to scavenge free radicals. Unfortunately, information on its antioxidant properties is missing or unreliable. Here, we report detailed quantum chemical results for ATV and its ortho- and para-hydroxy metabolites (o-ATV, p-ATV) in the methanolic phase. They comprise global reactivity indices, bond order indices, and spin densities as well as all relevant enthalpies of reaction (bond dissociation BDE, ionization IP and electron attachment EA, proton detachment PDE and proton affinity PA, and electron transfer ETE). With these properties in hand, we can provide the first theoretical explanation of the experimental finding that, due to their free radical scavenging activity, ATV hydroxy metabolites rather than the parent ATV, have substantial inhibitory effect on LDL and the like. Surprisingly (because it is contrary to the most cases currently known), we unambiguously found that HAT (direct hydrogen atom transfer) rather than SPLET (sequential proton loss electron transfer) or SET-PT (stepwise electron transfer proton transfer) is the thermodynamically preferred pathway by which o-ATV and p-ATV in methanolic phase can scavenge DPPH• (1,1-diphenyl-2-picrylhydrazyl) radicals. From a quantum chemical perspective, the ATV's species investigated are surprising because of the nontrivial correlations between bond dissociation energies, bond lengths, bond order indices and pertaining stretching frequencies, which do not fit the framework of naive chemical intuition.

Negative Ion Photoelectron Spectra of Deprotonated Benzonitrile Isomers via Computation of Franck-Condon Factors

Negative ion photoelectron spectra of ortho (o-), meta (m-), and para (p-) deprotonated benzonitrile (o-, m-, p-C₆H₄(CN)^-) isomers as well as the associated thermochemical values corresponding to deprotonation at o-, m-, and p-positions in C₆H₅(CN) are presented. Quantum mechanical results based on the density functional theory (DFT) utilizing the aug-cc-pVQZ basis set indicate that the o-, m-, p-C₆H₄(CN)^● radicals have electron affinity values (EAs) of 1.901, 1.778, and 1.789 eV, respectively. The computed Franck-Condon (FC) factors give rise to o-, m-, and p-C₆H₄(CN)^- negative ion spectra with FC active ring distortion vibrational modes with harmonic vibrational frequencies of ∼450, 760, and 1000 cm^-1 as the dominant vibrational progressions. Deprotonation at the o-, m-, and p-positions in C₆H₅(CN) results in calculated gas-phase acidity values (Δ_acidH_298K^o) of 383.9, 385.7, and 385.3 kcal mol^-1, respectively. The calculated Δ_acidH_298K^o is in close agreement with the previously reported high-pressure mass spectrometry experimental value of 383.4.0 ± 4.4 kcal mol^-1. The computed Δ_acidH_298K^o and EAs are utilized to estimate the bond dissociation energy (DH₂₉₈(H-C₆H₄CN)) associated with the formation o-, m-, and p-C₆H₄(CN)^● using the negative ion thermochemical cycle: DH₂₉₈(C₆H₅CN) = Δ_acidH_298K^o (H-C₆H₄(CN) + EA (C₆H₅CN)^● - IP(H). The respective values of DH₂₉₈(H-C₆H₄CN) corresponding to the formation of ortho, meta, and para C₆H₄(CN) radicals are 114.15, 113.11, and 113.51 kcal mol^-1.

Nitriles with High Gas-Phase Basicity-Part II Transmission of the Push-Pull Effect through Methylenecyclopropene and Cyclopropenimine Scaffolds Intercalated between Different Electron Donor(s) and the Cyano N-Protonation Site

This work extends our earlier quantum chemical studies on the gas-phase basicity of very strong N-bases to two series of nitriles containing the methylenecyclopropene and cyclopropenimine scaffolds with dissymmetrical substitution by one or two electron-donating substituents such as Me, NR2, N=C (NR2)2, and N=P (NR2)3, the last three being strong donors. For a proper prediction of their gas-phase base properties, all potential isomeric phenomena and reasonable potential protonation sites are considered to avoid possible inconsistencies when evaluating the energetic parameters and associated protonation or deprotonation equilibria B + H+ = BH+. More than 250 new isomeric structures for neutral and protonated forms are analyzed. The stable structures are selected and the favored ones identified. The microscopic (kinetic) gas-phase basicity parameters (PA and GB) corresponding to N sites (cyano and imino in the cyclopropenimine or in the substituents) in each isomer are calculated. The macroscopic (thermodynamic) PAs and GBs, referring to the isomeric mixtures of favored isomers, are also estimated. The total (pushing) substituent effects are analyzed for monosubstituted and disubstituted derivatives containing two identical or two different substituents. Electron delocalization is examined in the two π-π conjugated transmitters, the methylenecyclopropene and cyclopropenimine scaffolds. The aromatic character of the three-membered ring is also discussed.

Benchmark ab initio proton affinity and gas-phase basicity of α-alanine based on coupled-cluster theory and statistical mechanics

We determine the proton affinity (PA) and gas-phase basicity (GB) of amino acid α-alanine at a chemically accurate level by performing explicitly-correlated CCSD(T)-F12b/aug-cc-pVDZ geometry optimizations and normal mode vibrational frequency calculations as well as CCSD(T)-F12b/aug-cc-pVTZ energy computations at the possible neutral and protonated geometries. Temperature effects at 298.15 K considering translational, rotational, and vibrational enthalpy and entropy corrections are obtained via standard statistical mechanics utilizing the molecular geometries and the harmonic vibrational energy levels. Both the amino nitrogen (N) and the carbonyl oxygen (O) atoms are proven to be potential protonation sites and a systematic conformational search reveals 3 N- and 9 O-protonated conformers in the 0.00-7.88 and 25.43-30.43 kcal/mol energy ranges at 0 K, respectively. The final computed PA and GB values at (0)298.15 K in case of N-protonation are (214.47)216.80 and 207.07 kcal/mol, respectively, whereas the corresponding values for O-protonation are (189.04)190.63 and 182.31 kcal/mol. The results of the benchmark high-level coupled-cluster computations are utilized to assess the accuracy of several lower-level cost-effective methods such as MP2 and density functional theory with various functionals (SOGGA11-X, M06-2X, PBE0, B3LYP, M06, TPSS).

A Mechanistic Study on the Formation of Dronic Acids

Dronic acid derivatives, important drugs against bone diseases, may be synthesized from the corresponding substituted acetic acid either by reaction with phosphorus trichloride in methanesulfonic acid as the solvent or by using also phosphorous acid as the P-reactant if sulfolane is applied as the medium. The energetics of the two protocols were evaluated by high-level quantum chemical calculations on the formation of fenidronic acid and benzidronic acid. The second option, involving (HO)₂P-O-PCl₂ as the nucleophile, was found to be more favorable over the first variation, comprising Cl₂P-O-SO₂Me as the real reagent, especially for the case of benzidronate.

Structures, binding energies and non-covalent interactions of furan clusters

Understanding of the furan solvent is subjected to the knowledge of the structures of the furan clusters and interactions taking place therein. Although, furan clusters can be very important to determine the dynamics and the properties of the furan solvent, there has been only a few investigations reported on furan dimer. In this work, we have explored the potential energy surfaces (PESs) of the furan clusters using two incremental levels of theory. Structures have been initially generated using classical molecular dynamics followed by full optimization at the MP2/aug-cc-pVDZ level of theory. The results show that the most stable structure of the furan dimer has a stacking configuration while that of the trimer has a cyclic configuration. We have noted that the structures of the furan tetramer have no definite configurations. In addition, we have performed a quantum theory of atoms in molecule (QTAIM) analysis to identify all possible non-covalent interactions of the furan clusters. The results show that six different types of non-covalent interactions can be identified in furan clusters. We have noted that the CH⋯C and CH⋯O hydrogen bondings are the strongest non-covalent interactions while the H⋯H bonding interaction is found to be the weakest. Furthermore, we have assessed the performance of ten DFT functionals in calculating the binding energies of the furan clusters. The ten DFT functionals (M05, M05-2X, M06, M06-2X, M08HX, PBE0, ωB97XD, PW6B95D3, APFD and MN15) have been benchmarked to DLPNO-CCSD(T)/CBS. The functionals M05-2X and M06 are recommended for further affordable investigations of the furan clusters.

Push–Pull Effect on the Gas-Phase Basicity of Nitriles: Transmission of the Resonance Effects by Methylenecyclopropene and Cyclopropenimine π-Systems Substituted by Two Identical Strong Electron Donors

The gas-phase basicity of nitriles can be enhanced by a push–pull effect. The role of the intercalated scaffold between the pushing group (electron-donor) and the pulling (electron-acceptor) nitrile group is crucial in the basicity enhancement, simultaneously having a transmission function and an intrinsic contribution to the basicity. In this study, we examine the methylenecyclopropene and the N-analog, cyclopropenimine, as the smallest cyclic π systems that can be considered for resonance propagation in a push–pull system, as well as their derivatives possessing two strong pushing groups (X) attached symmetrically to the cyclopropene scaffold. For basicity and push–pull effect investigations, we apply theoretical methods (DFT and G2). The effects of geometrical and rotational isomerism on the basicity are explored. We establish that the protonation of the cyano group is always favored. The push–pull effect of strong electron donor X substituents is very similar and the two π-systems appear to be good relays for this effect. The effects of groups in the two cyclopropene series are found to be proportional to the effects in the directly substituted nitrile series X–C≡N. In parallel to the basicity, changes in electron delocalization caused by protonation are also assessed on the basis of aromaticity indices. The calculated proton affinities of the nitrile series reported in this study enrich the gas-phase basicity scale of nitriles to around 1000 kJ mol−1.

Overestimation of 3α- over 3β-25-Hydroxyvitamin D3 Levels in Serum: A Mechanistic Rationale for the Different Mass Spectral Properties of the Vitamin D Epimers

The metabolism of vitamin D₃ includes a parallel C-3 epimerization pathway-in addition to the standard metabolic processes for vitamin D₃-reversing the stereochemical configuration of the -OH group at carbon-3 (β→α). While the biological function of the 3α epimer has not been elucidated yet, the additional species cannot be neglected in the analytical determination of vitamin D₃, as it has the potential to introduce analytical errors if not properly accounted for. Recently, some inconsistent mass spectral behavior was seen for the 25-hydroxyvitamin D₃ (25(OH)D₃) epimers during quantification using electrospray LC-MS/MS. The present work extends that of Flynn et al. ( Ann. Clin. Biochem. 2014, 51, 352-559) and van den Ouweland et al. ( J. Chromatogr. B 2014, 967, 195-202), who reported larger electrospray ionization response factors for the 3α epimer of 25(OH)D₃ in human serum samples as compared to the regular 3β variant. The present work was concerned with the mechanistic reasons for these differences. We used a combination of electrospray ionization, atmospheric pressure chemical ionization, and density functional theory calculations to uncover structural dissimilarities between the epimers. A plausible mechanism is described based on intramolecular hydrogen bonding in the gas phase, which creates a small difference of proton affinities between the epimers. More importantly, this mechanism allows the explanation of the different ionization efficiencies of the epimers based on kinetic control of the ionization process, where ionization initially takes place at the hydroxyl group with subsequent proton transfer to a basic carbon atom. The barrier for this transfer differs between the epimers and is in direct competition with H₂O elimination from the protonated hydroxyl group. The "hidden" site of high gas phase basicity was revealed through computational calculations and appears to be inaccessible via direct protonation.

Quantum-Chemical Search for Keto Tautomers of Azulenols in Vacuo and Aqueous Solution

Keto-enol prototropic conversions for carbonyl compounds and phenols have been extensively studied, and many interesting review articles and even books appeared in the last 50 years. Quite a different situation takes place for derivatives of biologically active azulene, for which only scanty information on this phenomenon can be found in the literature. In this work, quantum-chemical studies have been undertaken for symmetrically and unsymmetrically substituted azulenols (constitutional isomers of naphthols). Stabilities of two enol (OH) rotamers and all possible keto (CH) tautomers have been analyzed in the gas phase {DFT(B3LYP)/6-311+G(d,p)} and also in aqueous solution {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. Contrary to naphthols, for which the keto forms can be neglected, at least one keto isomer (C1H, C2H, and/or C3H) contributes significantly to the tautomeric mixture of each azulenol to a higher degree in vacuo (non-polar environment) than in water (polar amphoteric solvent). The highest amounts of the CH forms have been found for 2- and 5-hydroxyazulenes, and the smallest ones for 1- and 6-hydroxy derivatives. The keto tautomer(s), together with the enol rotamers, can also participate in deprotonation reaction leading to a common anion and influence its acid-base properties. The strongest acidity in vacuo exhibits 6-hydroxyazulene, and the weakest one displays 1-hydroxyazulene, but all azulenols are stronger acids than phenol and naphthols. Bond length alternation in all DFT-optimized structures has been measured using the harmonic oscillator model of electron delocalization (HOMED) index. Generally, the HOMED values decrease for the keto tautomers, particularly for the ring containing the labile proton. Even for the keto tautomers possessing energetic parameters close to those of the enol isomers, the HOMED indices are low. However, some kind of parallelism exists for the keto forms between their relative energies and HOMEDs estimated for the entire molecules.

Temperature-dependent oxidation of BSCAPE molecule in methanol medium

Temperature-dependent solvation free energy and oxidation by free energy of ionization of 2-Phenylethyl (2E)-3-(1-benzenesulfonyl-4,5-dihydroxyphenyl) acrylate (BSCAPE) in methanol medium are the concerns of the present work. This molecule is a relevant phenolic acid enclosing multiple bioactivities. The explicit, implicit and discrete-continuum models of solvation were used. The methanol molecules were coordinated to this acid to form cluster complexes. The dual method M06-2X/6-31++G(d,p)//B3LYP/6-31G(d) was employed along with basis set superposition error correction. The results show that, the free energy of coordination and solvation are distant. Both quantities increase with temperature. From discrete-continuum treatment, there is non-spontaneity of solvation process, while coordination yielded spontaneity and non-spontaneity at cold and hot room temperatures, respectively. The ionization potential in gas phase, decreases with temperature. All the solvation models yielded lower ionization potential than that of gas phase. Thus, it follows that, the increase of temperature and methanol medium favours the oxidation of BSCAPE. Consequently, this favours its metabolism processes.

Structures and relative stability of hydrated ferrous ion clusters and temperature effects

Structures of solvated ferrous ion clusters have been investigated in the singlet and quintet spin states of the ferrous ion. Relative stabilities of isomers are also discussed at different temperatures.

Understanding the solubilization of Ca acetylide with a new computational model for ionic pairs

The unique reactivity of the acetylenic unit in DMSO gives rise to ubiquitous synthetic methods. We theoretically consider CaC2 solubility and protolysis in DMSO and formulate a strategy for CaC2 activation in solution-phase chemical transformations. For this, we use a new strategy for the modeling of ionic compounds in strongly coordinating solvents combining Born-Oppenheimer molecular dynamics with the DFTB3-D3(BJ) Hamiltonian and static DFT computations at the PBE0-D3(BJ)/pob-TZVP-gCP level. We modeled the thermodynamics of CaC2 protolysis under ambient conditions, taking into account its known heterogeneity and considering three polymorphs of CaC2. We give a theoretical basis for the existence of the elusive intermediate HC[triple bond, length as m-dash]C-Ca-OH and show that CaC2 insolubility in DMSO is of thermodynamic nature. We confirm the unique role of water and specific properties of DMSO in CaC2 activation and explain how the activation is realized. The proposed strategy for the utilization of CaC2 in sustainable organic synthesis is outlined.

Gas-Phase Protonation Thermodynamics of Biological Lipids: Experiment, Theory, and Implications

Phospholipids are important to cellular function and are a vital structural component of plasma and organelle membranes. These membranes isolate the cell from its environment, allow regulation of the internal concentrations of ions and small molecules, and host diverse types of membrane proteins. It remains extremely challenging to identify specific membrane protein-lipid interactions and their relative strengths. Native mass spectrometry, an intrinsically gas-phase method, has recently been demonstrated as a promising tool for identifying endogenous protein-lipid interactions. However, to what extent the identified interactions reflect solution- versus gas-phase binding strengths is not known. Here, the "Extended" Kinetic Method and ab initio computations at three different levels of theory are used to experimentally and theoretically determine intrinsic gas-phase basicities (GB, ΔG for deprotonation of the protonated base) and proton affinities (PA, ΔH for deprotonation of the protonated base) of six lipids representing common phospholipid types. Gas-phase acidities (ΔG and ΔH for deprotonation) of neutral phospholipids are also evaluated computationally and ranked experimentally. Intriguingly, it is found that two of these phospholipids, sphingomyelin and phosphatidylcholine, have the highest GB of any small, monomeric biomolecules measured to date and are more basic than arginine. Phosphatidylethanolamine and phosphatidylserine are found to be similar in GB to basic amino acids lysine and histidine, and phosphatidic acid and phosphatidylglycerol are the least basic of the six lipid types studied, though still more basic than alanine. Kinetic Method experiments and theory show that the gas-phase acidities of these phospholipids are high but less extreme than their GB values, with phosphatidylserine and phosphatidylglycerol being the most acidic. These results indicate that sphingomyelin and phosphatidylcholine lipids can act as charge-reducing agents when dissociated from native membrane protein-lipid complexes in the gas phase and provide a straightforward model to explain the results of several recent native mass spectrometry studies of protein-lipid complexes.

Understanding the Photo- and Electro-Carboxylation of o-Methylbenzophenone with Carbon Dioxide

The lack of understanding of the radical reaction mechanism of Carbon dioxide (CO2) in photo- and electro-catalysis results in the development of such applications far behind the traditional synthesis methods. Using methylbenzophenone as the model, we clarify and compare the photo-enolization/Diels−Alder (PEDA) mechanism for photo-carboxylation and the two-step single-electron reduction pathway for electro-carboxylation with CO2 through careful control experiments. The regioselective carboxylation products, o-acylphenylacetic acid and α-hydroxycarboxylic acid are obtained, respectively, in photo- and electro-chemistry systems. On the basis of understanding the mechanism, a one-pot step-by-step dicarboxylation of o-methylbenzophenone is designed and conducted. Both the experimental results and related density functional theory (DFT) calculation verify the feasibility of the possible pathway in which electro-carboxylation is conducted right after photo-carboxylation in one vessel. This synthesis approach may provide a mild, eco-friendly strategy for the production of polycarboxylic acids in industry.

Purine tautomeric preferences and bond-length alternation in relation with protonation-deprotonation and alkali metal cationization

Quantum chemical calculations were carried out for deprotonated (P-) and protonated purine (PH+) and for adducts with one alkali metal cation (P-M+ and PM+, where M+ is Li+ or Na+) in the gas phase {B3LYP/6-311+G(d,p)}, a model of perfectly apolar environment, and for selected structures in aqueous solution {PCM(water)//B3LYP/6-311+G(d,p)}, a reference polar medium for biological studies. All potential isomers of purine derivatives were considered, the favored structures indicated, and the preferred sites for protonation/deprotonation and cationization reactions determined. Proton and metal cation basicities of purine in the gas phase were discussed and compared with those of imidazole and pyrimidine. Bond-length alternations in the P, PH+, P-M+, and PM+ forms were quantitatively measured using the harmonic oscillator model of electron delocalization (HOMED) indices and compared with those for P. Variations of the HOMED values when proceeding from the purine structural building blocks, pyrimidine and imidazole, to the bicyclic purine system were also examined. Generally, the isolated NH isomers exhibit a strongly delocalized π-system (HOMED > 0.8). Deprotonation slightly increases the HOMED values, whereas protonation and cationization change the HOMED indices in different way. For bidentate M+-adducts, the HOMED values are larger than 0.9 like for the largely delocalized P-. The HOMED values correlate well in a comprehensive relationship with the relative Gibbs energies (ΔG) calculated for individual isomers whatever the purine form is, neutral, protonated, or cationized. When PCM-DFT model was utilized for P-, PH+, PM+, and P-M+ (M+ = Li+) both electron delocalization and relative stability are different from those for the molecules in vacuo. The solvation effects cause a slight increase in HOMEDs, whereas the ΔEs decrease, but in different ways. Hence, contribution of particular isomers in the isomeric mixtures of PH+, PM+, and P-M+ also varies. HOMED variations for the favored neutral, deprotonated, protonated, and lithiated forms of purine in the gas phase and aqueous solution.

Large-Sized Ammonia Clusters and Solvation Energies of the Proton in Ammonia

The absolute solvation energies (free energies and enthalpies) of the proton in ammonia are used to compute the pK_a of species embedded in ammonia. They are also used to compute the solvation energies of other ions in ammonia. Despite their importance, it is not possible to determine experimentally the solvation energies of the proton in a given solvent. We propose in this work a direct approach to compute the solvation energies of the proton in ammonia from large-sized neutral and protonated ammonia clusters. To undertake this investigation, we performed a geometry optimization of neutral and protonated ammonia 30-mer, 40-mer, and 50 mer to locate stable structures. These structures have been fully optimized at both APFD/6-31++g(d,p) and M06-2X/6-31++g(d,p) levels of theory. An infrared spectroscopic study of these structures has been provided to assess the reliability of our investigation. Using these structures, we have computed the absolute solvation free energy and the absolute solvation enthalpy of the proton in ammonia. It comes out that the absolute solvation free energy of the proton in ammonia is calculated to be -1192 kJ mol^-1 , whereas the absolute solvation enthalpy is evaluated to be -1214 kJ mol^-1 . © 2019 Wiley Periodicals, Inc.