The role of weak interactions in lignin polymerization.

Lignin is the most abundant natural polymer composed by aromatic moieties. Its chemical composition and its abundance have focused efforts to unlock its potential as a source of aromatic compounds for many years. The lack of a proper way for lignin de-polymerization has hampered its success as a natural solution for commodity aromatic chemicals, which is also due to the lack of understanding of the underlying mechanisms of lignin polymerization. A fuller fundamental understanding of polymerization mechanisms could lead to improvements in de-polymerization strategies, and therefore a proper methodology and a predictive theoretical framework are required for such purpose. This work presents a complete computational study on some of the key steps of lignin polymerization mechanisms. Density functional theory (DFT) calculations have been performed to evaluate the most appropriate methodology and to compute the chemical structures and reaction enthalpies for the monolignol dimerization, the simplest key step that controls the polymerization. Quantum theory of atoms in molecules (QTAIM) has been applied to understand the coupling reaction mechanisms, for which the radical species and transition states (TSs) involved have been characterized. The coupling that leads to the formation of the ß-O-4 linkage has been theoretically reproduced according to proposed mechanisms, for which weak interactions have been found to play a key role in the arrangement of reactants. The hydrogen bond formed between the oxygen of the phenoxy radical, and the alcohol of the aliphatic chain, together with the interaction between aromatic rings, locates the reactants in a position that favors such ß-O-4 linkage. Graphical Abstract QTAIM analysis of the complex between coumaryl and coniferyl alcohols. It emphasizes the importance of weak interactions during the formation of beta-O-4 linkages in the polymerization of lignin.

A computational study of bulk porous two-dimensional polymers related to graphyne.

Over the last twelve years there has been an explosion in the area of reticular chemistry with several classes of carbonaceous or carbon-rich reticular compounds coming into the scene and/or suffering an exponential growth in the number of related studies. Examples are MOFs, COFs, graphene and 2D polymers. π-Conjugated reticular compounds in particular are of great interest due to their optoelectronic properties. In this study we use density functional theory methods with periodic boundary conditions to investigate the stacking arrangements of bulk 2D polymer multilayer porous graphyne A, the related carbon allotrope multilayer graphyne B, and the analog bulk 2D polymer C in which the triple bonds of A are substituted by double bonds. The results show that for the three materials the eclipsed stacking arrangements are considerably less stable than staggered and slipped arrangements, with the more stable structures being slipped, staggered and off-centered-staggered arrangements for A, B and C, respectively. To shed light on the π-π interactions responsible for the geometry and relative energies of the different stacking modes we analyze the topology of the electron density using the electron localization function. In addition, simulated patterns for powder X-ray diffraction have been obtained from the optimized systems, which can be used for identification of the bulk 2D reticular compounds in future syntheses.

Regioselective enzymatic acylations of polyhydroxylated eudesmanes: semisynthesis, theoretical calculations, and biotransformation of cyclic sulfites.

Different lipase enzymes have been tested in order to perform regioselective acetylations on the eudesmane tetrol from vulgarin. High yields (95%) of 1,12-diacetoxy derivative (4) were achieved in 1 h with Candida antarctica lipase (CAL). However, only the 12-acetyl derivative (6) was obtained in similar yield with Mucor miehei (MML) or Candida cylindracea (CCL) lipases. The enzymatic protection at C-1 and C-12 has been used to form eudesmane cyclic-sulfites between C-6 and C-4 atoms. The R/S-sulfur configuration has been assigned by means of the experimental and theoretical (13)C and (1)H NMR chemical shifts. The theoretical shifts were calculated using the GIAO method, with a MM+ geometry optimization followed by a single-point calculation at the B3LYP/6-31G(*) level (B3LYP/6-31G(*)//MM+). Moreover, B3LYP/6-31G(*) geometry optimizations were carried out to test the B3LYP/6-31G(*)//MM+ results, for the deacetylated sulfites (12 and 15). In addition to the delta(C) and delta(H) shifts, the (3)J(HH) coupling constants were also calculated and compared with the experimental values when available. Finally, different reactivities have been checked in both sulfites by biotransformation with Rhizopus nigricans. While the R-sulfite gave 2 alpha- and 11 beta-hydroxylated metabolites, the S-sulfite yielded only regioselective deacetylations. Furthermore, both sulfites showed different reactivities in redox processes.

On the aromaticity and Meisenheimer rearrangement of strained heterocyclic amine, phosphine, and arsine oxides.

A theoretical investigation (AIM and ELF analyses together with NMR chemical shifts) has been conducted for three-membered heterocycle (N, P, and As) oxides. An aromatic stabilization was found for the P and As rings. However, the N derivatives displayed a net negative hyperconjugation in the N-O bond formation, without ring aromaticity observed for their electronic properties. The calculated delta(C) and delta(H) shifts also supported the ring delocalization for the P and As unsaturated heterocycle oxides (delta(C) approximately 165 and delta(H) approximately 9 ppm). In addition, these values for 1H-azirine oxide resembled standard C=C double bond values (delta(C) approximately 130 and delta(H) approximately 7 ppm). The different behavior for the N oxides was also observed in their Meisenheimer rearrangement (MR). All the reaction paths, yielding the corresponding hydroxyl structures, were exothermic (G2 method). However, the N derivatives showed the lowest values for activation enthalpy, DeltaH(). The C=C bond influence in the MR was slight, with the same DeltaH values for the saturated and unsaturated paths. This rearrangement for the P and As oxides yielded TSs closer to the reactives; however, the corresponding TSs resembled the products for the N-derivatives. The different reaction paths have been examined by their corresponding AIM and ELF analyses at the B3LYP/6-311G level.

Multiple bonding in four-coordinated titanium(IV) compounds.

Theoretical description (MP2/6-311G* and B3LYP/6-311G*) is presented for hypovalent titanium alkoxide model compounds showing linear angleTi-O-C angles. This feature is explained by the existence of a polarized triple Ti-O bond. In contrast, a series of 18 electron germanium derivatives displaying bent angleGe-O-C angles contain polarized single Ge-O bonds. The nature of the Ti-O and Ge-O bonds is established by means of natural bond order, atoms-in-molecules theory, and electron localization function analyses.

Theoretical Bonding Description of Alkylidene Chalcogen (O, S, Se) Difluorides (H(2)C=XF(2)): Planar versus Bent Conformations.

Theoretical descriptions of alkylidene chalcogen difluorides have been performed on their planar (1-3) and bent (4-6) conformations. The planar T-shaped conformations were the most stable ones, from the calculations performed (Gaussian-G2 and B3LYP/6-311+G). The bonding nature of the T-shaped (C(2)(v)()) structures has also been analyzed by means of the atoms in molecules (AIM) theory and electron localization function analyses.