Computer modelling of the conformational equilibrium of 2-and 2,5,5-substituted 1,3,2-dioxaborinanes

Empirical, semiempirical, and nonempirical quantum-chemical methods were used to study the conformational equilibrium of 2,5,5-substituted 1,3,2-dioxaborinanes. The sofa invertomers were found to correspond to the local and global minima on the potential energy surface. The position of the equilibrium between these forms is a function of the substituents at C₍₅₎ of the heterocycle. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1860–1865, December, 2007.     

Conductometric study of cationic and anionic complexes in propylene carbonate

Conductivity data are used to determine thermodynamic complex formation constants for cases in which both the initial electrolyte and the complexed electrolyte form ion pairs. Using the method described in the text, the complex formation constants of Li⁺, Na⁺ and K⁺ with the crown ether 18-crown-6 and of Li⁺ with the ligand triphenylphosphine oxide in propylene carbonate have been evaluated from conductance data. The complexation of AgBr in propylene carbonate solutions of n-etrabutylammonium bromide has also been studied by the measurement of molar conductivities. The results of these studies indicate that ion pairing should not be neglected, even in high permittivity solvents such as propylene carbonate, and that the ion pair association constants correlate well with structural studies on cation-crown ether molecular conformations.     

Coulombic Basis for Relative Hydrogen-Bonding Basicities and Conformational Energies of Tertiary Amine Oxides and Phosphine Oxides

The structures, energies, and natural atomic charges of 2-dimethylaminophenol oxide, 2-Me₂N-(O)C₆H₄OH, and 2-dimethylphosphinylphenol, 2-Me₂P(O)C₆H₄OH, in three different conformations were computed at the ab initio MP2/6-31G* level. Computed natural charges indicate distributions of electron density in amine oxides and phosphine oxides that are quite different from what is normally assumed on the basis of the formal charges in the usual representations of these compounds. The charges on nitrogen and phosphorus in these compounds are typically computed to be approximately zero on nitrogen and +2 on phosphorus, and the oxygen is considerably more negative in the phosphine oxide than in the amino oxide. Electronegativity differences thus play a larger role and formal charges a smaller one in determining atomic charges in these compounds than is generally believed. Despite the more negative oxygen in phosphine oxides, amine oxides are computed to be considerably more basic when participating in hydrogen bonding. Calculations treating the computed natural charges on these six conformations as point charges for classical approximations of the coulombic energies support the idea that the quantum mechanically computed relative energies are largely determined by coulombic interactions.     

Possible conformations and relative stability of the 7-membered ring in 1α,5β,6,7α(H)-and 1β,5α,6,7α(H)-guai-11(13)-en-6,12-olides

Stereoisomers of 1,5,6,7(H)- and 1,5,6,7(H)-guai-11(13)-en-6,12-olides are calculated using molecular mechanics. The possibility of forming various conformations in the 7-membered ring is examined as a function of the fusion to the 5-membered C-ring. The effect of the methyl orientation on the conformation of the 7-membered ring and the relative stability of the conformers are discussed.Insitute of Phytochemistry, Karaganda, fax (3212)-43-37-73. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 54–56, January–February, 2000.     

Intramolecular co-operative hydrogen bond in calix[<Emphasis Type="Italic">n</Emphasis>]arenes (<Emphasis Type="Italic">n</Emphasis> = 4, 6, 8) bearing bulky substituents

Based on the Fourier transform IR spectroscopy together with the published NMR and X-ray data, it was shown that cyclic co-operative intramolecular hydrogen bond in calix[n]arene (n = 4, 6, 8) molecules is mainly responsible for their conformational state irrespective of the presence or absence of bulky substituents at the upper rim of the molecules. In accordance with the size of a macrocycle (n = 4, 6, 8), the stable conformation, secured by such a hydrogen bond, constitutes a cone, a pinched cone, and a pleated loop, respectively. The new, potentially competing system of hydrogen bonds in calix[6]arenes with 3-carboxymethyl-1-adamantyl substituents does not affect the conformational state of the macrocycle and its H-bonding. Six carboxy groups at the upper rim form in pairs three cyclic dimers, which does not disturb the hydrogen bonds of the hydroxy groups and the conformation of the macrocycle. In addition, the cavity of the molecule is considerably enlarged. The removal or rearrangement of the guest molecules in the solid calixarene by heating up to 180 °C only slightly affects the conformational state of macrocycles bearing bulky substituents, whereas in calixarenes devoid of such substituents, the similar procedure leads to somewhat of a distortion of the macrocycles (judging from the IR spectral indications of hydrogen bonding). Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1062–1068, June, 2007.     

Symmetry numbers and chemical reaction rates

This article shows how to evaluate rotational symmetry numbers for different molecular configurations and how to apply them to transition state theory. In general, the symmetry number is given by the ratio of the reactant and transition state rotational symmetry numbers. However, special care is advised in the evaluation of symmetry numbers in the following situations: (i) if the reaction is symmetric, (ii) if reactants and/or transition states are chiral, (iii) if the reaction has multiple conformers for reactants and/or transition states and, (iv) if there is an internal rotation of part of the molecular system. All these four situations are treated systematically and analyzed in detail in the present article. We also include a large number of examples to clarify some complicated situations, and in the last section we discuss an example involving an achiral diasteroisomer.     

Structure and Electronic Properties of Fullerenes C52q+: Is C522+ an Exception to the Pentagon Adjacency Penalty Rule?

The structure, vibrational spectra and electronic properties of the neutral, singly and doubly charged C52 fullerenes were studied by means of the Hartree-Fock method and density functional theory. Different isomers were considered, in particular those with the lowest possible number (five or six) of adjacent pentagons, and an isomer with a four-atom ring. For neutral and singly charged species, the most stable isomer is that with the lowest number of adjacent pentagons, namely five. However, for C(52)2+, the most stable structure has six adjacent pentagons. This finding, which contradicts the pentagon adjacency penalty rule, is a consequence of complete filling of the HOMO pi shell and the near-perfect sphericity of the most stable isomer. The simulated vibrational spectra show important differences in the positions and intensities of the vibrations for the different isomers.     

Conformational flexibility of xanthene‐based covalently linked dimers

The conformational flexibility of three covalently linked dimers consisting of two xanthene‐based moieties connected by a diphenyl ether linker was studied using NMR spectroscopy, X‐ray crystallography, and density functional theory (DFT) calculations. The three dimers interconvert as a function of pH: the doubly cationic dimer (Xan⁺)₂ exists in acidic solutions (pH < 0.5), the mono‐alcohol monocation Xan⁺–Xan‐OH at intermediate pH values (pH = 1–3), and the neutral diol at the highest pH‐values (pH > 3). Each dimer exhibits conformational degrees of freedom associated with rotations of either the xanthene moiety or of the diphenyl ether (DPE) linker. The barriers for rotation of the xanthylium moiety were evaluated using DFT calculations, yielding values of 23 kcal/mol for (Xan⁺)₂ and 11 kcal/mol for (Xan‐OH)₂, respectively. The rotational barrier for the diphenyl ether linker in Xan⁺–Xan‐OH (15 kcal/mol) was experimentally determined using variable temperature NMR measurements. The relative orientation of the two –OH groups in (Xan‐OH)₂ diol was investigated in solution and the solid state using NMR spectroscopy and X‐ray crystallography. The conformer observed in the solid state was found to be the In–Out conformer, while free rotation of the xanthenol units is thought to occur on the NMR timescale at room temperature. These studies are relevant for the design of linkers for efficient water oxidation catalysts. Copyright © 2016 John Wiley & Sons, Ltd.     

Mechanistic aspects of the dehydration and dehydrohalogenation of halo-hydroxyformaldoxime conformers. A quantum chemical model study

A detailed exploration of the configurational and conformational space of chloro- and bromo-hydroxyformaldoximes, Xhfaox (X = Cl, Br) has been carried out with the aid of the B3LYP level of density functional theory, using the 6-31G(d,p) basis set. The most stable configuration in each series of the Clhfaox and Brhfaox conformers corresponds to the Z-s-cis, s-trans configuration, while the highest energy Z-(s-trans, s-cis) conformers were found at 7.0(7.6) and 6.0(6.6) kcal mol(-1), respectively, at the B3LYP(QCISD(T)) levels of theory. Saddle points were also located on the PES of the Clhfaox and Brhfaox compounds corresponding to Z-(s-cis, s-cis) conformers at 13.8(14.9) and 13.6(14.6) kcal mol(-1), respectively, at the B3LYP(QCISD(T)) levels. Upon dehydration Xhfaox could afford a number of isomeric CXNO species. The dehydration processes of Xhfaox are predicted to be endothermic, the computed heats of reactions found in the range of 20.5 to 86.2 kcal mol(-1) and 15.9 to 100.4 kcal mol(-1) at the B3LYP and QCISD(T) levels, respectively. The reaction pathways for the addition of water to halo-fulminates yielding the most stable Xhfaox conformers was predicted to be concerted with a single transition structure, but are asynchronous with activation barriers of 32.8 and 43.0 kcal mol(-1) for the chloro- and bromo-derivatives, respectively. The PES governing the isomerization reactions of the CXNO isomers have also been calculated, and possible isomerization pathways have been delineated. Upon dehydrohalogenation the Xhfaox conformers yield hydroxy-isocyanate or hydroxy-fulminate, the former being more stable by 31.8(18.8) kcal mol(-1) at the B3LYP(QCISD(T)) levels of theory. The reaction pathways for the addition of HX to hydroxy-isocyanate were predicted to be slightly exothermic, the heats of reactions being -3.2 and -5.5 kcal mol(-1), respectively, and have to surmount high activation barriers of 39.7 and 35.0 kcal mol(-1), respectively. Similarly, the addition of HX to hydroxy-fulminate was predicted to be much more exothermic, the heats of reactions being -34.7 and -37.3 kcal mol(-1), respectively, and have to surmount much lower activation barriers of only 10.5 and 7.5 kcal mol(-1) respectively, at the B3LYP level. Finally, calculated structures, relative stability, and bonding properties of all stationary points located on the PES of the systems and reactions studied are thoroughly discussed with respect to computed electronic properties.     

Infrared spectral study of molecular vibrations in amorphous, nanocrystalline and AlO(OH) · αH2O bulk crystals

Amorphous, nanocrystalline, and bulk AlO(OH) · xH₂O crystals have six fundamental modes (FM) of vibration in a nonlinear AlO(OH) molecular structure. Most of them appear in groups of four IR and Raman bands. Their positions and relative intensities differ significantly in three specimens. The nanocrystals (monoclinic structure with z=8 molecules per unit cell) have four OH stretching bands at values enhanced by up to 360 cm⁻¹ at 3120, 3450, 3560 cm⁻¹ in comparison to those in bulk crystals or amorphous specimens. The first two bands are broad, bandwidth Δν_1/2200 to 350 cm⁻¹, while the other two are sharp, Δν_1/290 cm⁻¹. The sharp bands shift to 3525 and 3595 cm⁻¹ after heating the sample at 100°C. They no longer appear after heating at 300 or 500°C for 2 h (the specimen decomposes to Al₂O₃), leaving behind only two bands at 3100 and 3400 cm⁻¹. A Δν_1/2 value of 500 cm⁻¹ appears in the 3400 cm⁻¹ in a delocalized distribution of H atoms. Two bands also occur at 3098 and 3300 cm⁻¹ in bulk crystals (orthorhombic structure with z=4) or at 2990 and 3515 cm⁻¹ in an amorphous sample. More than one bands appear in a FM vibration in occurrence of sample in more than one conformers. The amorphous sample has approximately the same conformer structure as the bulk crystals. An amorphous surface structure exists in nanocrystals with a group of three bands at 1420, 1510 and 1635 cm⁻¹ in an interconnected network structure. It encapsulates the nanocrystals in an amorphous shell. Its volume fraction, 33% estimated from the integrated intensity in three bands, determines 2.2 nm thickness in the shell in spherical shape of nanocrystals in 35 nm diameter.