Application of Free-Wilson matrices to the analysis of the tautomerism and aromaticity of azapentalenes: a DFT study

(Pyridin-2-ylmethyl)triel Derivatives as Masked Frustrated Lewis Pairs. Interactions and CO2 -Sequestration

The isolated (pyridin-2-ylmethyl)triel derivatives (triel=B, Al and Ga) show an intramolecular N⋅⋅⋅Tr triel bond as shown by compounds found in the Cambridge Structural Database and DFT calculations. The possibility to use them as masked frustrated Lewis pairs (mFLP) has been explored theoretically concerning their reaction with CO2 . The adduct formation proceeds in two steps. In the first one, the (pyridin-2-ylmethyl)triel derivatives break the intramolecular N⋅⋅⋅Tr bond assisted by CO2 and in the second step the adduct is formed with Tr-O and N-C covalent bonds. The corresponding energy minima and transition states (TS) of the reaction have been characterized and analyzed. The distortion/interaction model analysis of the stationary points indicates that the whole process can be divided in two parts: reorganization of the mFLP in the first steps of the reaction while the reaction with CO2 (associated to the distortion of this molecule) is more important in the formation of the final adduct. In all cases studied, the final products are more stable than the starting molecules that combine with reasonable TS energies indicating that these reactions can occur.

The SN2 reaction and its relationship with the Walden inversion, the Finkelstein and Menshutkin reactions together with theoretical calculations for the Finkelstein reaction

This communication gives an overview of the relationships between four reactions that although related were not always perceived as such: SN2, Walden, Finkelstein, and Menshutkin. Binary interactions (SN2 & Walden, SN2 & Menshutkin, SN2 & Finkelstein, Walden & Menshutkin, Walden & Finkelstein, Menshutkin & Finkelstein) were reported. Carbon, silicon, nitrogen, and phosphorus as central atoms and fluorides, chlorides, bromides, and iodides as lateral atoms were considered. Theoretical calculations provide Gibbs free energies that were analyzed with linear models to obtain the halide contributions. The M06-2x DFT computational method and the 6-311++G(d,p) basis set have been used for all atoms except for iodine where the effective core potential def2-TZVP basis set was used. Concerning the central atom pairs, carbon/silicon vs. nitrogen/phosphorus, we reported here for the first time that the effect of valence expansion was known for Si but not for P. Concerning the lateral halogen atoms, some empirical models including the interaction between F and I as entering and leaving groups explain the Gibbs free energies.

Alkali Metal Cations Bonding to Carboxylate Anions: Studies using Mass Spectrometry and Quantum Chemical Calculations

Data on the gas-phase energetics of anion/cation interactions are relatively scarce. In this work, gas-phase alkali metal cation basicity (AMCB) scales were established for a series of 15 benzoate ions XC₆H₄COO^- with Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺ on the basis of mass spectrometry experiments and high-level calculations. A wide range of electron-donating and electron-withdrawing substituents were included in the study. The thermochemical values were calculated by ab initio methodologies and extrapolated to the complete basis set limit. For each metal cation, the experimental relative cation basicity values of the anions were established quantitatively by applying the Cooks' kinetic method to the cation-bound heterodimers [(XC₆H₄COO^-)M⁺(YC₆H₄COO^-)]^-, generated by electrospray ionization. The self-consistency of these AMCB scales was ascertained by multiple overlap of the individual relative basicities. In parallel, the proton gas-phase basicities (GBs) of the benzoate anions (gas-phase acidities of the respective benzoic acids) were calculated in order to compare the results of the theoretical method with known experimental GB values. The experimental and calculated GB values agree quite accurately (average absolute deviation = 3.2 kJ mol^-1). The relative experimental AMCB scales and the absolute calculated AMCB scales are highly correlated, and the two sets agree by better than 4 kJ mol^-1. It is also demonstrated that the five series of calculated AMCBs are highly correlated with the calculated GB.

An experimental and computational NMR study of organometallic nine-membered rings: Trinuclear silver(I) complexes of pyrazolate ligands

This work reports the calculation of the nuclear magnetic resonance (NMR) chemical shifts of eight trinuclear Ag(I) complexes of pyrazolate ligands using the relativistic program ZORA. The data from the literature concern exclusively ¹ H, ¹³ C, and ¹⁹ F nuclei. For this reason, one of the complexes that is derived from 3,5-bis-trifluoromethyl-1H-pyrazole has been studied anew, and the ¹⁵ N and ¹⁰⁹ Ag chemical shifts determined for the first time in solution. Solid-state NMR data of this compound have been obtained for some nuclei (¹ H, ¹³ C, and ¹⁹ F) but not for others (¹⁴ N, ¹⁵ N, and ¹⁰⁹ Ag).

Non-bonding interactions and non-covalent delocalization effects play a critical role in the relative stability of group 12 complexes arising from interaction of diethanoldithiocarbamate with the cations of transition metals Zn(II), Cd(II), and Hg(II): a theoretical study

The chelating properties of diethanoldithiocarbamate (DEDC) and π-electron flow from the nitrogen atom to the sulfur atom via a plane-delocalized π-orbital system (quasi ring) was studied using a density functional theory method. The molecular structure of DEDC and its complexes with Zn(II), Cd(II), and Hg(II) were also considered. First, the geometries of this ligand and DEDC-Zn(II), DEDC-Cd(II), and DEDC-Hg(II) were optimized, and the formation energies of these complexes were then calculated based on the electronic energy, or sum of electronic energies, with the zero point energy of each species. Formation energies indicated the DEDC-Zn(II) complex as the most stable complex, and DEDC-Cd(II) as the least stable. Structural data showed that the N1-C2 π-bond was localized in the complexes rather than the ligand, and a delocalized π-bond over S7-C2-S8 was also present. The stability of DEDC-Zn(II), DEDC-Cd(II), and DEDC-Hg(II) complexes increased in the presence of the non-specific effects of the solvent (PCM model), and their relative stability did not change. There was π-electron flow or resonance along N1-C2-S7 and along S7-C2-S8 in the ligand. The π-electron flow or resonance along N1-C2-S7 was abolished when the metal interacted with sulfur atoms. Energy belonging to van der Waals interactions and non-covalent delocalization effects between the metal and sulfur atoms of the ligand was calculated for each complex. The results of nucleus-independent chemical shift (NICS) indicated a decreasing trend as Zn(II) < Cd(II) < Hg(II) for the aromaticity of the quasi-rings. Finally, by ignoring van der Waals interactions and non-covalent delocalization effects between the metal and sulfur atoms of the ligand, the relative stability of the complexes was changed as follows:[Formula: see text] Graphical Abstract Huge electronic cloud localized on Hg(II) in the Hg(II)-DEDC complex.

Influence of fluoro and cyano substituents in the aromatic and antiaromatic characteristics of cyclooctatetraene

An exhaustive and systematic study of the structural and electronic properties of cyclooctatetraene (COT) upon substitution of hydrogen atoms by fluoro and cyano groups has been carried out in order to analyse the influence of both substituents on the aromaticity.

Gas-phase lithium cation basicity: revisiting the high basicity range by experiment and theory

According to high level calculations, the upper part of the previously published FT-ICR lithium cation basicity (LiCB at 373 K) scale appeared to be biased by a systematic downward shift. The purpose of this work was to determine the source of this systematic difference. New experimental LiCB values at 373 K have been measured for 31 ligands by proton-transfer equilibrium techniques, ranging from tetrahydrofuran (137.2 kJ mol(-1)) to 1,2-dimethoxyethane (202.7 kJ mol(-1)). The relative basicities (ΔLiCB) were included in a single self-consistent ladder anchored to the absolute LiCB value of pyridine (146.7 kJ mol(-1)). This new LiCB scale exhibits a good agreement with theoretical values obtained at G2(MP2) level. By means of kinetic modeling, it was also shown that equilibrium measurements can be performed in spite of the formation of Li(+) bound dimers. The key feature for achieving accurate equilibrium measurements is the ion trapping time. The potential causes of discrepancies between the new data and previous experimental measurements were analyzed. It was concluded that the disagreement essentially finds its origin in the estimation of temperature and the calibration of Cook's kinetic method.

Methods for building QSARs

Structure-activity relationship (SAR) and quantitative structure-activity relationship (QSAR) models are increasingly used in toxicology, ecotoxicology, and pharmacology for predicting the activity of the molecules from their physicochemical properties and/or their structural characteristics. However, the design of such models has many traps for unwary practitioners. Consequently, the purpose of this chapter is to give a practical guide for the computation of SAR and QSAR models, point out problems that may be encountered, and suggest ways of solving them. Attempts are also made to see how these models can be validated and interpreted.

Annular tautomerism: experimental observations and quantum mechanics calculations

The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein-small molecule crystal structures.

Molecular recognition studies on naphthyridine derivatives

The association constants K_b of three hosts I–III designed to have both enhanced hydrogen bonding donor strength and conformational preorganization with biotin analogues 1–5 are reported. ¹H-NMR titrations under two different concentration conditions have been employed to determine the association constants K_b. A statistical analysis using a presence absence matrix has been applied to calculate the different contributions. Hydrogen bond interactions make naphthyridine derivatives II and III potent binders and effective receptors for (+)-biotin methyl ester (1), due to the complex stabilization by additional hydrogen bonds.

Difluorobenzenes revisited: an experimental and theoretical study of spin-spin coupling constants for 1,2-, 1,3-, and 1,4-difluorobenzene

The experimental spin-spin coupling constants (SSCCs) for 1,3- and 1,4-difluorobenzene have been determined anew, and found to be consistent with previously determined values. SSCCs for 1,2-, 1,3-, and 1,4-difluorobenzene have been analyzed by comparing them with the coupling constants computed using the second-order polarization propagator approximation (SOPPA) and the equation-of-motion coupled cluster singles and doubles method (EOM-CCSD). Eighty experimental values have been analyzed using SOPPA calculations, and a subset of 40 values using both SOPPA and EOM-CCSD approaches. One-bond coupling constants (1)J(C-C) and (1)J(C-F) are better described by EOM-CCSD, whereas one-bond (1)J(C-H) values are better described by SOPPA. An empirical equation is presented which allows for the prediction of unknown coupling constants from computed SOPPA values. A similar approach may prove useful for predicting coupling constants in larger systems.

A theoretical study of the neutral and the double-charged cation of cyclo[8]pyrrole and its interaction with inorganic anions

A theoretical study of the complexation of cyclo[8]pyrrole dication, 2, and the corresponding system in neutral form, 3, with six anionic molecules has been carried out up to the B3LYP/6–311++G(2d,2p) computational level. The effect of the water solvation has been taken into account by means of the PCM method. The gas phase results correspond to the very large interaction energies expected for the interaction of molecules of opposite charge. In all the complexes, the analysis of the electron density by means of the Atoms In Molecules (AIM) methodology shows the presence of eight intermolecular interactions between the individual molecules. The results, using the water solvent model, indicate that the 2:SO42− complex is more stable than the 2:NO3−, in agreement with experimental results.

A theoretical structural analysis of the factors that affect (1)J(NH), (1h)J(NH) and (2h)J(NN) in N-H...N hydrogen-bonded complexes

Calculations of (1)J(NH), (1h)J(NH) and (2h)J(NN) spin-spin coupling constants of 27 complexes presenting N-H...N hydrogen bonds have allowed to analyze these through hydrogen-bond coupling as a function of the hybridization of both nitrogen atoms and the charge (+1, 0, - 1) of the complex. The main conclusions are that the hybridization of N atom of the hydrogen bond donor is much more important than that of the hydrogen bond acceptor. Positive and negative charges (cationic and anionic complexes) exert opposite effects while the effect of the transition states 'proton-in-the-middle' is considerable.