isodesmic reactions
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2021 ◽  
Author(s):  
Croix Laconsay ◽  
Tyler Rho ◽  
Dean Tantillo

Hyperconjugation/conjugation through-bond stereoelectronic effects were studied with density functional theory (DFT) in the context of 3-azabicyclo[3.3.1]nonanes to unravel puzzling differences in reactivity between a vinylogous chloride (4) and a vinylogous ester (5). These compounds—whose structures differ only by one substituent—were found to display strikingly different reactivities in hydrochloric acid by Risch and co-workers (J. Am. Chem. Soc. 1991, 113, 9411–9412). Computational analyses of substituent effects, noncovalent interactions, natural bond orbitals, isodesmic reactions, and hydration propensities lead to a model for which the role of remote, through-bond stereoelectronic effects is key to explaining 4 and 5’s diverging reactivity.


2021 ◽  
Vol 22 (16) ◽  
pp. 8595
Author(s):  
Dóra Papp ◽  
Imola Csilla Szigyártó ◽  
Bengt Nordén ◽  
András Perczel ◽  
Tamás Beke-Somfai

Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol−1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol−1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol−1 per residue excess stabilization.


Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3556
Author(s):  
Al Mokhtar Lamsabhi ◽  
Otilia Mó ◽  
Manuel Yáñez

An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH2(CH2)nCH2NH2 (n = 0–5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH2(CH2)nCH2NH2 (n = 0–3) interact with BeF2. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.


Author(s):  
Татьяна Александровна Савицкая ◽  
Екатерина Александровна Шахно ◽  
Иван Павлович Босько ◽  
Вадим Эдвардович Матулис ◽  
Наталья Анатольевна Мелеховец ◽  
...  

Water-insoluble polyelectrolyte complexes of cellulose acetate sulphate in the form of sodium salt (Na-CAS) and aminoglycoside antibiotic (AB) kanamycin (KAN) were obtained by mixing of the components aqueous solutions. The composition of the complexes was determined in accordance with the medium pH and mixing order. The increase of Na‑CAS cellobiose units per mole of AB has been shown to correlate with the decrease of pH value. The complex formation was studied by Fourier transform infrared spectroscopy, thermal analysis, X-ray analysis, laser diffraction, motion trajectory of nanoparticles analysis and scanning electron microscopy. Quantum-chemical study of the relative stability of the protonated forms of KAN in aqueous solution was performed to determine the preferred protonation sites of KAN molecule. The pKa values of KAN were calculated by means of isodesmic reactions method. The structures and binding energy for the KAN dimer and the KAN – CAS complex were also investigated by quantum-chemical methods. Na‑CAS – KAN complex itself and immobilised on the activated carbon was shown to demonstrate in vitro two times antibacterial activity of the standard (injectable) form of KAN against Mycobacterium tuberculosis. It can be recommended for in vivo clinical trials as a new form of aminoglycoside AB for oral administration.


Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5836
Author(s):  
Alexander A. Larin ◽  
Dmitry M. Bystrov ◽  
Leonid L. Fershtat ◽  
Alexey A. Konnov ◽  
Nina N. Makhova ◽  
...  

In the present work, we studied in detail the thermochemistry, thermal stability, mechanical sensitivity, and detonation performance for 20 nitro-, cyano-, and methyl derivatives of 1,2,5-oxadiazole-2-oxide (furoxan), along with their bis-derivatives. For all species studied, we also determined the reliable values of the gas-phase formation enthalpies using highly accurate multilevel procedures W2-F12 and/or W1-F12 in conjunction with the atomization energy approach and isodesmic reactions with the domain-based local pair natural orbital (DLPNO) modifications of the coupled-cluster techniques. Apart from this, we proposed reliable benchmark values of the formation enthalpies of furoxan and a number of its (azo)bis-derivatives. Additionally, we reported the previously unknown crystal structure of 3-cyano-4-nitrofuroxan. Among the monocyclic compounds, 3-nitro-4-cyclopropyl and dicyano derivatives of furoxan outperformed trinitrotoluene, a benchmark melt-cast explosive, exhibited decent thermal stability (decomposition temperature >200 °C) and insensitivity to mechanical stimuli while having notable volatility and low melting points. In turn, 4,4′-azobis-dicarbamoyl furoxan is proposed as a substitute of pentaerythritol tetranitrate, a benchmark brisant high explosive. Finally, the application prospects of 3,3′-azobis-dinitro furoxan, one of the most powerful energetic materials synthesized up to date, are limited due to the tremendously high mechanical sensitivity of this compound. Overall, the investigated derivatives of furoxan comprise multipurpose green energetic materials, including primary, secondary, melt-cast, low-sensitive explosives, and an energetic liquid.


2019 ◽  
Author(s):  
Oscar Ventura ◽  
Martina Kieninger ◽  
Zoi Salta ◽  
Agnie M. Kosmas ◽  
Vincenzo Barone

<p></p><p>The reaction of toluene (T) with OH<sup>●</sup> produces addition products as well as the benzyl radical (TR). TR can react with OH<sup>●</sup> or O<sub>2</sub> to produce oxygenated species, for many of which there is no experimental information available. We present here theoretically determined heats of formation (HFs) of 17 such species using the non-isodesmic reactions on the potential energy surface (PES) of TR+O<sub>2</sub> and T+OH<sup>●</sup>+O<sub>2</sub>. For those species the experimental HFs of which are known, we obtained a good correlation between experimental and theoretical values at the G4 (r<sup>2</sup>=0.999) and M06/cc-pVQZ (r<sup>2</sup>=0.997) levels, thus showing the goodness of the methods used. Previously unknown HFs of other radicals (benzyloxyl, spiro [1,2-dioxetane benzyl], hydroxyphenyl, and benzylperoxyl) and closed shell species (salicylic alcohol, benzo[b]oxetane and p-hydroxy cyclohexa-2,5-dienone) were later determined using those methods.<b></b></p><br><p></p>


2019 ◽  
Author(s):  
Oscar Ventura ◽  
Martina Kieninger ◽  
Zoi Salta ◽  
Agnie M. Kosmas ◽  
Vincenzo Barone

<p></p><p>The reaction of toluene (T) with OH<sup>●</sup> produces addition products as well as the benzyl radical (TR). TR can react with OH<sup>●</sup> or O<sub>2</sub> to produce oxygenated species, for many of which there is no experimental information available. We present here theoretically determined heats of formation (HFs) of 17 such species using the non-isodesmic reactions on the potential energy surface (PES) of TR+O<sub>2</sub> and T+OH<sup>●</sup>+O<sub>2</sub>. For those species the experimental HFs of which are known, we obtained a good correlation between experimental and theoretical values at the G4 (r<sup>2</sup>=0.999) and M06/cc-pVQZ (r<sup>2</sup>=0.997) levels, thus showing the goodness of the methods used. Previously unknown HFs of other radicals (benzyloxyl, spiro [1,2-dioxetane benzyl], hydroxyphenyl, and benzylperoxyl) and closed shell species (salicylic alcohol, benzo[b]oxetane and p-hydroxy cyclohexa-2,5-dienone) were later determined using those methods.<b></b></p><br><p></p>


2019 ◽  
Vol 2019 ◽  
pp. 1-23 ◽  
Author(s):  
Kenneth Irving ◽  
Martina Kieninger ◽  
Oscar N. Ventura

The performance of a group of density functional methods of progressive complexity for the description of the ClO bond in a series of chlorine oxides was investigated. The simplest ClO radical species and the two isomeric structures XClO/ClOX for each X = H, Cl, and O were studied using the PW91, TPSS, B3LYP, PBE0, M06, M06-2X, BMK, and B2PLYP functionals. Geometry optimizations and reaction enthalpies and enthalpies of formation for each species were calculated using Pople basis sets and the (aug)-cc-pVnZ Dunning sets, with n = D, T, Q, 5, and 6. For the calculation of enthalpies of formation, atomization and isodesmic reactions were employed. Both the precision of the methods with respect to the increase of the basis sets, as well as their accuracy, were gauged by comparing the results with the more accurate CCSD(T) calculations, performed using the same basis sets as for the DFT methods. The results obtained employing composite chemical methods (G4, CBS-QB3, and W1BD) were also used for the comparisons, as well as the experimental results when they are available. The results obtained show that error compensation is the key for successful description of molecular properties (geometries and energies) by carefully selecting the method and basis sets. In general, expansion of the one-electron basis set to the limit of completeness does not improve results at the DFT level, but just the opposite. The enthalpies of formation calculated at the CCSD(T)/aug-cc-pV6Z for the species considered are generally in agreement with experimental determinations and the most accurate theoretical values. Different sources of error in the calculations are discussed in detail.


2018 ◽  
Author(s):  
Oscar Ventura ◽  
Martina Kieninger ◽  
Zoi Salta ◽  
Agnie M. Kosmas

<p>Reaction of toluene (T) with HO<sup>●</sup> produces addition products and the benzyl radical (TR). TR can react with HO<sup>●</sup> or O<sub>2</sub> to produce oxygenated species, for many of which there is no experimental information. We present here theoretically determined heats of formation (HFs) of 17 such species using non-isodesmic reactions of TR+O<sub>2</sub> and T+HO<sup>●</sup>+O<sub>2</sub>. For experimentally known HFs, we obtained a reasonable correlation between experimental and theoretical data for G4 (r2=0.999) and M06/cc-pVQZ (r2=0.997) results. Previously unknown HFs of other radicals (benzyloxy, spiro [1,2-dioxetane benzyl], hydroxyphenyl, and benzylperoxy) and closed shell species (salicylic alcohol, benzo[b]oxetane and p-hydroxy cyclohexa-2,5-dienone) were calculated using these methods. The species studied and the enthalpies of formation obtained were: salycilic alcohol, -69.7 ± 3.4 kcal/mol; benzyloxy radical, 28.4 ± 3.4 kcal/mol; hydroxyphenyl radical, 37.3 ± 3.4 kcal/mol; benzo[b]oxetane, 23.7 ± 3.4 kcal/mol; spiro [1,2-oxoetane phenyl] radical, 57.3 ± 3.4 kcal/mol; p-hydroxy cyclohexan-2,5-dienone, -42.1 ± 3.4 kcal/mol; and benzylperoxy radical, 28.5 ± 3.2 kcal/mol.</p>


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