Urea Decomposition Mechanism by Dinuclear Nickel Complexes.

Urease is an enzyme containing a dinuclear nickel active center responsible for the hydrolysis of urea into carbon dioxide and ammonia. Interestingly, inorganic models of urease are unable to mimic its mechanism despite their similarities to the enzyme active site. The reason behind the discrepancy in urea decomposition mechanisms between inorganic models and urease is still unknown. To evaluate this factor, we synthesized two bis-nickel complexes, [Ni2L(OAc)] (1) and [Ni2L(Cl)(Et3N)2] (2), based on the Trost bis-Pro-Phenol ligand (L) and encompassing different ligand labilities with coordination geometries similar to the active site of jack bean urease. Both mimetic complexes produced ammonia from urea, (1) and (2), were ten- and four-fold slower than urease, respectively. The presence and importance of several reaction intermediates were evaluated both experimentally and theoretically, indicating the aquo intermediate as a key intermediate, coordinating urea in an outer-sphere manner. Both complexes produced isocyanate, revealing an activated water molecule acting as a base. In addition, the reaction with different substrates indicated the biomimetic complexes were able to hydrolyze isocyanate. Thus, our results indicate that the formation of an outer-sphere complex in the urease analogues might be the reason urease performs a different mechanism.

Morphogenesis in Synthetic Chemical Cells.

We present an efficient model for describing morphogenesis and the emergence of spatiotemporal structures in synthetic chemical cells. This work is motivated by an experimental setup used for testing Turing's theory of morphogenesis. The model developed is based on the general theory of chemically active droplets, which combines the classical theory of phase separation with reaction-diffusion systems. Through the 2D calculations, we find the six spatiotemporal structures predicted by Turing in 1952 and experimentally observed, in a 1D array of droplets. Moreover, under Turing instability, with a determined chemical wavelength, the system undergoes morphogenesis. This theoretical approach provides a useful tool for understanding the physical differentiation through the direct calculation of the osmotic pressure in each cell as the chemical reaction occurs.

Chiral symmetry conservation principle.

We show a chiral symmetry conservation principle based on chemical kinetics using stochastic results. Suppose the chiral symmetry conservation is evoked, and our universe can be considered globally asymmetric. In that case, there are at least two mirrored asymmetric universes if all the chiral properties are strongly correlated. However, if the chiral correlations are weak or nonexistent, there are possibly Many-(Chiral-Symmetry)-Worlds. Alternatively, if our universe is only locally asymmetric, there could be a single universe with segregated chiral regions. The possible mechanisms of the primordial chiral symmetry breaking can only be found if the chiral symmetry is not truly conserved by assuming the initial racemic conditions. In that case, our universe is asymmetric and could be alone. On the other hand, if the chiral symmetry is conserved, there is no chance of finding the primordial chiral symmetry breaking. Based on this conservation (or not), it is possible to infer two opposite hypotheses, where two general scenarios about the chiral universes are possible.

Turing patterns modulation by chemical gradient in isothermal and non-isothermal conditions.

The modulation of Turing patterns through Dirichlet boundary conditions has been studied through the isothermal and non-isothermal versions of a Brusselator-like model in a small-size domain reactor. We considered the Minkowski functional and the rate of entropy production to characterize the morphological aspects of the patterns and to indicate transitions of spatial states. We find that boundary conditions can induce the spatial symmetry breaking of Turing patterns when they are defined around the equilibrium points of a homogeneous dynamical system. As a result, two different Turing patterns can emerge in a reactor under an imposed gradient of chemicals that contains the equivalent concentration of the equilibrium points at some point in the boundary.

Boron-nitrogen dative bond.

This study consists of the theoretical analysis of some organic molecules and their inorganic similar compounds, through substitution of two carbon atoms by boron and nitrogen atoms. The methods DFT/B3-LYP/TZVPP and CC2/TZVPP were considered. Firstly, ethane, ethene, and ethyne molecules (based on C atoms and their BN/NB analogs) were studied. These molecules were considered as a reference for the analysis of other molecules with functional groups. These molecules with functional groups are: ethanol, ethanal (and its isomer ethenol), ethanoic acid (and its isomer ethenediol), ethylamine, ethylbenzene, propane, and fluoroethane. We studied the energies, bond length, population analysis, and bond order. The dative bonds (BN) are bigger and weaker than that covalent based on C atoms. The dative bond has π character when the BN bond is double and triple. It is possible to distinguish two different behaviors for BN bonds, one when the functional group is bounded to the B atom, and the other to the N atom. When the functional group is bounded to the B atom, the BN bond is weaker and lengthier than that when the same group is bounded to the N atom. However, the isomer with weaker BN bond is the most stable one. Graphical abstract Comparative studies of dative bonds among substituted inorganic molecules, e.g., BN-ethanol, show important differences in terms of length and energy in comparison to organic analogous. There is also a difference when comparing BN or NB molecules (according to witch atom the functional group is bonded to, B or N); bond length, for example, is bigger for BN molecules.

On the degradation pathway of glyphosate and glycine.

The degradation in water of the most widespread herbicide, glyphosate, is still under debate. Experimental disagreements on this process exist and there are only a few theoretical studies to support any conclusions. Moreover, the relationship between glyphosate and glycine is underestimated. Besides the structural similarity, glycine is a product of glyphosate degradation; hence, their studies are complementary. In this study, two mechanisms for the decomposition of the glyphosate molecule and glycine molecule in water are proposed. These mechanisms were explored by using quantum mechanical calculations. A combined microsolvation/PCM approach was employed to find and characterize their transition states, by which the reaction pathways were determined via the IRC method. The results have shown that the degradation processes might occur via a C-C bond cleavage, through a concerted mechanism, whereby the proton transfers and the CO2 detachments occur simultaneously. The second mechanism had two consecutive steps, a decarboxylation followed by the proton transfers. The water molecules served as a conduit for the proton transfers, away from the amine group (or the phosphonate, glyphosate case). Their function was to assist the reactions in a water-mediated decarboxylation. In these particular cases, the free energy of activation was 42.68 and 42.28 kcal mol-1 for the glycine structure and the glyphosate structure, respectively. These results agreed with the photodegradation and thermodegradation of glyphosate, as well as with the spontaneous decarboxylation of glycine. A concerted mechanism might be expected to yield C-P and C-N bond cleavages in the glyphosate molecule.

A previously undescribed hexapeptide His-Arg-Phe-Leu-Arg-His-NH2 from amphibian skin secretion shows CO2 and metal biding affinities.

A previously undescribed six residues long peptide His-Arg-Phe-Leu-Arg-His was identified and purified from the skin secretion of the amphibian Phyllomedusa centralis. A synthetic analogue carboxyamidated HRFLRH-NH2 showed structural changes induced by CO2 and metal ions in aqueous solution when analyzed by NMR. The present work reports NMR structures for the carboxyamidated hexapeptide in the presence CO2, Zn2+ and Cd2+, suggesting possible affinity regions on the polypeptide chain for each ligand. The NMR structures were optimized by DFT to identify probable biding sites of these species in the polypeptide structure. To our best knowledge, this is the first time that a putative CO2 binding site is described on a peptide structure obtained in aqueous conditions, at room temperature.

Stability and molecular properties of the boron-nitrogen alternating analogs of azulene and naphthalene: a computational study.

In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investigated boron-nitrogen naphthalene (boroazanaphthalene) and two isomers of boron-nitrogen azulene, 1,3,4,6,8-pentaaza-2,3a,5,7,8a-pentaboraazulene (BN-azulene) and 2,3a,5,7,8a-pentaaza-1,3,4,6,8- pentaboraazulene (NB-azulene), are stable systems. However, these molecules have different properties, i.e., different stability, dipole moment, and aromaticity based on the NICS approach. BN-naphthalene has a high dipole moment magnitude showing high polar character, while naphthalene is apolar. BN- and NB-azulene are weakly polar, while ordinary azulene is highly polar in character. Also, substitution of C atoms by B and N atoms decreases the aromaticity. In the case of NB-azulene, the seven-membered ring has anti-aromaticity behavior while both rings of BN-azulene exhibit aromaticity. We expect that the new theoretical data provided in this work will be useful in identifying and characterizing experimentally the compounds investigated, and in helping our understanding of the chemistry of boron-nitrogen molecules. Graphical abstract Boron-nitrogen alternating analogs of azulene. Spectral distinction between isomers.

Spontaneous Chiral Symmetry Breaking for Finite Systems.

Theoretical clues are desirable to help uncover the origin of bio-homochirality in life, as well as the mechanisms for the asymmetric production of functional chiral substances. Here, an open-to-matter reaction network based on a model proposed by Plasson et al. is studied. In the extended model, the statistical fluctuations lead the system to break chiral symmetry autonomously, that is, without any initial enantiomeric excess or external influence. In the stability diagrams, we observe regions of parameter space that correspond to racemic, homochiral, chiral oscillatory, and, to our knowledge, for the first time in a chiral model, chaotic regimes. The dependencies of the final concentrations of chiral substances on the parameters are determined analytically and discussed for both the racemic and homochiral regimes.

Theoretical characterization of the BN and BP coronenes by IR, Raman, and UV-VIS spectra.

Boron-nitrogen coronene (BNC) and boron-phosphorous coronene (BPC), not yet synthesized molecules and of possible interest for material science, are composed of six condensed rings of borazine and boraphosphabenzene molecules, respectively. They are similar to the carbon coronene molecule (CC). Moreover, CC and BNC are isoelectronic and the BPC is formally isoelectronic with respect to other coronenes, if only the valence electrons are considered. In this work, the BNC and BPC were theoretically characterized using IR, Raman, and UV-VIS spectroscopies. The coronenes studied have D(6h) and D(3h) symmetries for carbon and boron compounds, respectively. The calculated vibrational and electronic spectra for the CC are in good agreement with the experimental data, indicating that the calculations for BNC and BPC will be useful to identify these compounds, when synthesized. The main vibrational modes of the CC, BNC, and BPC are correlated. However, the BPC vibrational frequencies are substantially lower than the CC and BNC ones. The electronic ground state studies showed that the BPC has intermediate characteristics between the CC and BNC.