Relative Gibbs Energies Research Articles

ZnCl2-Based Deep Eutectic Solvent as Solvent-Catalyst in the Michael Addition Reaction of Pyrrole to Maleimide

The use of deep eutectic solvents (DESs) as catalysts presents indisputable advantages, for example, their simplicity of preparation, high biodegradability, and recyclability, as well as zero toxicity and their effectiveness as environmentally friendly reaction media. However, aspects related to their reactivity and catalytic activity are still unclear. In this work, we explore the versatility of ChCl/ZnCl2 DES in the formation of C-C bonds through the Michael-type addition of pyrrole to maleimide, where ChCl/ZnCl2 DES leads to catalysis and chelation of the substrates, thus describing a recommended method for the construction of C-C bonds with high atomic economy. We describe experimental and theoretical aspects that explain the ability of ChCl/ZnCl2 DES in the presence of water to act as a catalyst in the formation of C-C bonds between pyrrole and maleimide. The potential energy surface showed that the ChCl and the zinc-zincate species 2ZnCl2·3H2O, formed by the interaction between zinc chloride and water, decrease the relative free Gibbs energy values for all the species involved in the reaction mechanism (TSs, intermediates, product), favoring the kinetics and thermodynamics of the Michael addition.

Photochemical and Collision-Induced Cross-Linking in Stereochemically Distinct Scaffolds of Peptides and Nitrile Imines in Gas-Phase Ions.

Intramolecular cross-linking between peptides and nitrile-imine intermediates was studied in stereochemically distinct conjugates in which the reacting components were mounted on cis-1,2-cyclohexane and trans-1,4-cyclohexane scaffolds that we call 1,2-s-peptides and 1,4-s-peptides, respectively. The nitrile-imine intermediates were generated by N2 loss from 2,5-diaryltetrazole tags upon UV-photodissociation at 213 and 250 nm or by collision-induced dissociation, and further interrogated by CID and UVPD-MS3. Peptide fragment ion series originating from linear structures and macrocyclic cross-links were distinguished and used to quantify the cross-linking yields. The yields in MS2 varied between 27% for AAAG conjugates to 78% for GAAAK conjugates, depending on the peptide sequence. The CID-MS3 yields were in a 57-97% range, depending on the peptide sequence. Structures of 1,2-s-peptide and 1,4-s-peptide ions as well as several of their nitrile-imine intermediates and cross-links were investigated by high-resolution cyclic ion mobility in combination with Born-Oppenheimer molecular dynamics and density functional theory calculations. Matches between the experimental and calculated collision cross sections and ion relative Gibbs energies were used to assign peptide structures. Peptide conjugates C-terminated with Gly and Lys residues underwent cross-linking by the carboxyl group, as established by MS3 sequencing and corroborated by carboxyl blocking experiments that lowered the cross-linking yields. Peptide conjugates C-terminated with Arg also cross-linked via the side-chain guanidine group. A notable feature of the 1,4-s-peptide ions was the participation of low-energy twist-boat cyclohexane conformers that was enforced by strong hydrogen bonds between the peptide and nitrile imine.

Catalysis by [Ga4 L6 ]12- Metallocage on the Nazarov Cyclization: The Basicity of Complexed Alcohol is Key.

The Nazarov cyclization is investigated in solution and within K12 [Ga4 L6 ] supramolecular organometallic cage by means of computational methods. The reaction needs acidic condition in solution but works at neutral pH in the presence of the metallocage. The reaction steps for the process are analogous in both media: (a) protonation of the alcohol group, (b) water loss and (c) cyclization. The relative Gibbs energies of all the steps are affected by changing the environment from solvent to the metallocage. The first step in the mechanism, the alcohol protonation, turns out to be the most critical one for the acceleration of the reaction inside the metallocage. In order to calculate the relative stability of protonated alcohol inside the cavity, we propose a computational scheme for the calculation of basicity for species inside cavities and can be of general use. These results are in excellent agreement with the experiments, identifying key steps of catalysis and providing an in-depth understanding of the impact of the metallocage on all the reaction steps.

Structural and thermochemical consequences of prototropy and ionization for the biomolecule xanthine in vacuo

The complete prototropic tautomeric mixture for xanthine (X), one of intermediates of nucleic acids degradation, have been investigated for the first time. Fifteen NH and twenty-eight CH tautomers, including rotamers of OH groups, have been considered to select the most potential ones for one-electron oxidation (X → X+ + e) and one-electron reduction (X + e → X−). For selected isomers, thermochemistry of prototropy and redox processes have been studied at the DFT(B3LYP)/6–311+G(d,p) level. The DFT calculations provide a new important information on isomeric composition of redox forms (X+ and X−) and also on ionization processes for X in vacuo. Positive ionization favors the dioxo NH tautomer – the main form for X, but also, it increases the stability of one hydroxy-oxo isomer – neglected for X. Although the CH tautomers can be neglected for both X and X+, some of them have very low energies for X− and dramatically change tautomeric preferences. They seem to dictate thermochemistry of negative ionization. Variations of bonds lengths for selected neutral and ionized xanthine-isomers have been examined at the DFT level by employing the geometry-based HOMED (Harmonic Oscillator Model of Electron Delocalization) descriptor, recently extended for heterocompounds. The HOMED indices seem to be parallel to the relative Gibbs energies only for the dioxo NH and CH isomers. For the mono- and di-hydroxy forms, scatter plots exist.

Dispersions of carbon nanotubes by helical flavin surfactants: Solvent induced stability and chirality enrichment, and solvatochromism

Although solvent governed stability, selection and optical behavior of single walled carbon nanotubes (SWNTs) brought about by using specialized surfactants have importance in relation to various optoelectronic and biological applications, their origins and solvatochromism have not been thoroughly explored owing to the lack of ideal surfactant dispersing SWNTs. We show that solvent driven SWNT selection and solvatochromism occurs in SWNTs wrapped by two flavin derivatives in solvents with dielectric constants (ε) ranging from 2.3 to 80.4. Flavin-SWNT nanocomposite dispersions exhibit near-armchair and chirality-specific enrichment in lower ε aromatic solvents, and those with broader chirality selectivity are formed in higher ε solvents. Those trends are also observed by controlling flavin concentration. Consideration of optical spectra provides relative quantum yields of flavin-SWNT in each solvent, showing toluene and p-xylene dispersions as best owing to highly individualized SWNT. The selectivities and relative stabilities of the flavin-SWNT nanoconjugates are associated with the solubility parameter (δ), which controls the respective morphology of the side chains and the relative Gibbs energies of the nanoconjugates relative to those of the free flavin and SWNTs. Differences between δ of side chains vs. the media results in extended and collapsed side chain conformations in respective lower and higher ε solvents, leading to diameters (dt) selection of SWNT owing to diameter modulation of the isoalloxazine assembly. In addition, with increasing ε optical transitions of flavin/SWNT exhibit lower bathochromic shifts owing to a passivating role played by the isoalloxazine that does not take place with other surfactants. The results suggest new guidelines for the design of good SWNT dispersions that take into consideration self-association of the surfactant, conformations of side chains and the nature of the solvent.

(H,H)-Isomerism of cis- and trans-di[benzo]porphyrazines: Quantum chemical modeling within the framework of the DFT method

Quantum-chemical calculation of the molecular structures of potential isomeric (NNNN)- donoratomic macrocyclic tetradentate ligands, cis- and trans-di[benzo]porphyrazines, was carried out using the density functional theory (DFT) B3PW91/TZVP. It is noted that the first of these compounds can exist in four forms [so-called ([Formula: see text]-isomers], differing from each other by the mutual orientation of hydrogen atoms bonded to the nitrogen atoms, while the second compounds take the form of two similar isomers. The values of the most important bond lengths, bond and non-bond angles in each of these ([Formula: see text] -isomeric compounds, as well as the values of their relative energy, standard enthalpy, entropy, and Gibbs energy of formation are presented. It was found that the most stable among both cis- and trans-di[benzo]porphyrazines is the ([Formula: see text]-isomer with the trans-orientation of hydrogen atoms bonded to nitrogen atoms, while the ([Formula: see text] -isomers with cis-oriented hydrogen atoms for both of these compounds had significantly higher relative energies.

Fluxional bis(phenoxy-imine) Zr and Ti catalysts for polymerization

Bis(phenoxy-imine) complexes of zirconium or titanium, a type of Fenokishi-Imin catalysts, allow the production of polyethylenes with well-defined bimodal molecular weight distributions. Interestingly, by substitution of phenyl rings in the bis(phenoxy-imine) ligands by perfluorinated phenyl rings, the polymerization reaches a desired unimodal behavior. These catalysts have three isomers of similar energy that can be easily interconverted. It is likely that the bimodal behavior is due to the coexistence of more than one isomer in the reaction vessel. Here, we perform static and dynamic DFT calculations to understand the isomerization of the catalytic active species. We analyze the relative Gibbs energies of the different isomers and the barriers for the isomerization processes. Further characterization of the isomers is obtained through stereo maps, aromaticity measures, and NCI plots. Our results show that by changing the phenyl group by a perfluorinated phenyl ring, one of the isomers is particularly stabilized, thus explaining the unimodal behavior of the polyethylene production process.

Condensed-phase relative Gibbs free energy and E/Z descriptors for 2-acetylthiophene and 2-acetylthiophene-N1-phenyl thiosemicarbazones.

Thiosemicarbazones (TSCs) encompasses a class of compounds relevant in the pharmacological context. Their specific applicability varies in function of the appropriated chemical modification and their binding to different transition metals. In the present work, we apply current standards functionals, B3LYP and B97D, with triple zeta basis set quality, 6-311++G(d,p), to investigate the relative stability of the various possible spatial arrangements for 2-acetylthiophene and 2-acetylthiophene-N1-phenyl thiosemicarbazones, denoted ATTSC and ATTSC-Ph, respectively. The relative stability of neutral and deprotonated species at ethanol described by an implicit solvent model was investigated. For ATTSC, the relative Gibbs energy changed significantly upon deprotonation, and for ATTSC-Ph, a novel global minimum was identified. Based on the present study, deprotonation determines population in condensed-media. Such information, valid for ATTSC and ATTSC-Ph, can be crucial in studying other thiosemicarbazones.

The conversion of L-lysine into L-β-lysine: the role of 5'-deoxyadenosyl radical and water-a DFT study.

In the current study, we deal with the crucial role of 5'-deoxyadenosyl radical and water in the mechanism of the conversion of L-lysine into L-β-lysine. The DFT (density functional theory)-B3LYP method coupled with 6-31G(d) basis set has been performed to investigate the optimized structures of transition states (TSs) and intermediates (IMs) of two processes in water: (i) the attack of 5'-deoxyadenosyl radical to complex PLP-L-lysine and (ii) hydrolysis to liberate L-β-lysine. Meanwhile, M062X/6-311++g(3df,2p) level of theory is applied to compute the relative Gibbs energy ΔG. Procedure (i) has undergone various steps but includes two main structural aziridinyl rings TS2 (ΔG = 4.1kcal/mol) and TS3 (ΔG = 2.3kcal/mol). In stage (ii), hydroxy group of water would help to break the bond between β-NH2 group of L-lysine and PLP better than that of Tyr389.

A DFT Investigation on Two Proposed Anticancer Platinum(IV) Drugs

In our previous work, we illustrated that tetrachroridoplatinum(IV) complex with dipyridylamine (PtIVdpa) exhibited to be a selective cytotoxic drug, among a series of similar analogues in the in vitro study. In this research, by means of the Becke3LYP DFT functional calculations, PtIVdpa was compared with a known platinum(IV) drug, tetraplatin (PtIVdach), theoretically. The mechanism of two-electron reduction of PtIVdpa was followed thoroughly, in comparison with PtIVdach. The relative Gibbs energies for initial intermediate 5-coordinated [PtIV(dpa)Cl3]+ and also for the last product 4-coordinated [PtII(dpa)Cl2] is lower than those found for PtIVdach. However, since guanosine binds with platinum center, the relative energies become more for compounds with dpa than with dach. It seems the hydrogen bonds play a crucial role in the stability of intermediates and transition states.

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

Synthesis of Quaternary Carbon-Centered Benzoindolizidinones via Novel Photoredox-Catalyzed Alkene Aminoarylation: Facile Access to Tylophorine and Analogues

Photoredox-catalyzed aminoarylation and thioamination of unactivated alkenes have been developed, providing novel synthetic routes to access synthetically challenging quaternary carbon-centered ben...

Adsorption of Biomass-Derived Products on MoO3: Hydrogen Bonding Interactions under the Spotlight.

We performed a computational study on the interaction of O-containing compounds coming from biomass with a catalytic surface of MoO3. The addition of H atoms on the metal oxide surface mimics different scenarios of its exposure to the ambient or protons coming from biomass. Representative compounds from fatty acids (from triacylglycerides) and aromatics (from lignin) were adsorbed on the metal oxide surfaces. We covered the complete H surface coverage, and the adsorbed molecules showed structural changes due to the interactions in turn. The driven force interactions in this process is hydrogen bonding, which reveals the complexity in biomass processing. H-bonds were fully characterized by the electron density and its Laplacian where bond critical points are present. These topological properties allow us to understand the correlation between the adsorption energies and the strength on each adsorption site. We also computed the relative Gibbs energies and harmonic oscillator model of aromaticity index of the adsorbed molecules to get more insights into their stability.

Ab initio investigation of the lower-energy candidate structures for (H2O)10+ water cluster

Low-lying structures of water cationic clusters and the compounds with the OH radical have become a hot topic in recent years. We here investigate the cluster $$ {\left({\mathrm{H}}_2\mathrm{O}\right)}_{10}^{+} $$ and calculate its ideal structures by the quantum chemical calculation together with the particle swarm optimization method. We analyzed the properties of the obtained lower-energy isomers of $$ {\left({\mathrm{H}}_2\mathrm{O}\right)}_{10}^{+} $$ . Their energies are further re-optimized and demonstrated at three different methods with two basis sets. Based on our numerical calculations, a new cage-like structure of $$ {\left({\mathrm{H}}_2\mathrm{O}\right)}_{10}^{+} $$ with the lowest energy is obtained at MP2/aug-cc-pVDZ level. Our results showed the comparison of energy order at different conditions and demonstrated the influence of temperature on the relative Gibbs energy and IR spectra. Moreover, we also contained the molecule orbitals to discuss the stability of these representative isomers.

Understanding the Gas Phase Chemistry of Alkanes with First-Principles Calculations

Alkyl radicals are key intermediates in multiple industrially important reactions, including the dehydrogenation of alkanes. Because of their diverse chemistry, alkyl radicals form various products via a number of competing reactions in the gas phase. Using Density Functional Theory (DFT) and accurate ab initio electronic structure calculations (CBS-QB3), we investigated the thermodynamics and kinetics of gas phase alkyl radical reactions. Specifically, we investigated the hydrogen abstraction, radical recombination, and alkene formation reactions of light alkyl radicals (C1–C8). We show that the hydrogen abstraction Gibbs energies are correlated with the relative Gibbs energies of the corresponding radicals. On the basis of the reaction energy calculations, we identified that the competition between radical recombination reactions and alkene formation reactions is governed by the stability of the alkene products, with the alkene formation being preferred when more substituted alkenes are formed. It was f...

JESS, a Joint Expert Speciation System – VI: thermodynamically-consistent standard Gibbs energies of reaction for aqueous solutions

A large, open-access, sustainable database of relative Gibbs energies is developed for over 50 000 aqueous chemical species, including many metal–ligand complexes.

Electrochemical behavior of praseodymium and Pr-Al intermetallics in LiCl-KCl-AlCl3-PrCl3 melts

The electrochemical behavior of Pr(III) and formation process of Pr-Al intermetallics were investigated by different electrochemical methods. The reduction of Pr(III) ion to metallic Pr is an one-step three-electrons reaction. The reversibility of Pr(III)/Pr(0) system was evaluated by cyclic voltammograms with different scan rates. The co-reduction of Pr(III) and Al(III) ions formed three different Pr-Al intermetallics at electrode potentials around −1.40, −1.80, and −1.95 V vs. Ag/AgCl at 723 K, respectively. Open-circuit chronopotentiometry and electromotive force (emf) measurements were carried out to estimate the relative molar Gibbs energies of Pr for the formation of different Pr-Al intermetallics in the temperature range of 723–843 K. The activities of Pr in the Pr-Al intermetallic compounds were calculated.

Predicting Thermodynamic Properties of PBXTHs with New Quantum Topological Indexes

Novel group quantitative structure-property relationship (QSPR) models on the thermodynamic properties of PBXTHs were presented, by the multiple linear regression (MLR) analysis method. Four thermodynamic properties were studied: the entropy (Sθ), the standard enthalpy of formation (ΔfHθ), the standard Gibbs energy of formation (ΔfGθ), and the relative standard Gibbs energy of formation (ΔRGθ). The results by the formula indicate that the calculated and predicted data in this study are in good agreement with those in literature and the deviation is within the experimental errors. To validate the estimation reliability for internal samples and the predictive ability for other samples, leave-one-out (LOO) cross validation (CV) and external validation were performed, and the results show that the models are satisfactory.

1H NMR spectra of butane‐1,4‐diol and other 1,4‐diols: DFT calculation of shifts and coupling constants

The proton nuclear magnetic resonance (NMR) spectra of butane-1,4-diol, pentane-1,4-diol, (S,S)-hexane-2,5-diol, 2,5-dimethylhexane-2,5-diol and cyclohexane-1,4-diols (cis and trans) in benzene and some other solvents have been analysed. The conformer distribution and the NMR shifts of these diols in benzene have been computed on the basis of the density functional theory, the solvent being included by means of the integral-equation-formalism polarizable continuum model implemented in Gaussian 09. Relative Gibbs energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6-311+G(d,p) level and NMR shifts by the gauge-including atomic orbital method with the PBE0/6-311+G(d,p) geometry and the cc-pVTZ basis set. Vicinal three-bond coupling constants for the acyclic diols are calculated from the relative conformer populations, the geometries and generalized Karplus equations developed by Altona's group; these correlate well with the experimental values. The solvent dependence of coupling constants for butane-1,4-diol is attributed to conformational change. Coupling constants for the rigid cyclohexane-1,4-diols do not change with solvent and are readily explained in terms of their geometries. The NMR shifts of hydrogen-bonded protons in individual conformers of alkane-1,n-diols show a very rough correlation with the OH · · · OH distances. The computed overall NMR shifts for CH protons in 1,2-diols, 1,3-diols and 1,4-diols are systematically high but correlate very well with the experimental values, with a gradient of 1.07 ± 0.01; those for OH protons correlate less well.

Phase Competition in Bismuth Layered Structure Based on First Principles Thermodynamics

The difficulties of synthesis of pure Aurivillius phases largely impede them from extensive application. In this work, the first principles thermodynamics approach was applied to investigate the phase competition relation of three homologous Aurivillius series CaBi2Nb2O9-nNaNbO(3), Bi4Ti3O12-nSrTiO(3) and Bi4Ti3O12-nCaTiO(3), in order to uncover the thermodynamic mechanism of the phase stability. The competition among different phases was analyzed by the relative Gibbs energy as a function of chemical potential of perovskite unit. The analysis reveals that most phases are able to overcome others to be the most stable ones in a certain range as chemical potential increases, which can be applied to interpret the relevant experimental phenomena including the phase mixture and disordered structures. Temperature dependence of phase competition evolutions are also studied based on the configurational and vibrational entropy effect, the former effect changes the competition relations of different phases, while the latter only increases the stable range of the lower phases.