Investigating the interplay between charge transfer and CO2 insertion in the adsorption of a NiFe catalyst for CO2 electroreduction on a graphite support through DFT computational approaches.

This article describes a density functional theory (DFT) study to explore a bio-inspired NiFe complex known for its experimental activity in electro-reducing CO2 to CH4 when adsorbed on graphite. The coordination properties of the complex are investigated in isolated form and when physisorbed on a graphene surface. A comparative analysis of DFT approaches for surface modeling is conducted, utilizing either a finite graphene flake or a periodic carbon surface. Results reveal that the finite model effectively preserves all crucial properties. By examining predicted structures arising from CO2 insertion within the mono-reduced NiFe species, whether isolated or adsorbed on the graphene flake, a potential species for subsequent electro-reduction steps is proposed. Notably, the DFT study highlights two positive effects of complex adsorption: facile electron transfers between graphene and the complex, finely regulated by the complex state, and a lowering of the thermodynamic demand for CO2 insertion.

A bio-inspired heterodinuclear hydrogenase CoFe complex.

Herein, a new heterobimetallic CoFe complex is reported with the aim of comparing its performance in terms of H2 production within a series of related MFe complexes (M = Ni, Fe). The fully oxidized [(LN2S2)CoII(CO)FeIICp]+ complex (CoIIFeII, LN2S2 2- = 2,2'-(2,2'-bipyridine-6,6'-diyl)bis(1,1'-diphenylethanethiolate), Cp- = cyclopentadienyl anion) can be (electro)chemically reduced to its CoIFeII form, and both complexes have been isolated and fully characterized by means of classic spectroscopic techniques and theoretical calculations. The redox properties of CoIIFeII have been investigated in DMF, revealing that this complex is the easiest to reduce by one-electron among the analogous MFe complexes (M = Ni, Fe, Co). Nevertheless, it displays no electrocatalytic activity for H2 production, contrary to the FeFe and NiFe analogs, which have proven remarkable performance.

Crossing of the Cystic Barriers of Toxoplasma gondii by the Fluorescent Coumarin Tetra-Cyclopeptide.

FR235222 is a natural tetra-cyclopeptide with a strong inhibition effect on histone deacetylases, effective on mammalian cells as well as on intracellular apicomplexan parasites, such as Toxoplasma gondii, in the tachyzoite and bradyzoite stages. This molecule is characterized by two parts: the zinc-binding group, responsible for the binding to the histone deacetylase, and the cyclic tetrapeptide moiety, which plays a crucial role in cell permeability. Recently, we have shown that the cyclic tetrapeptide coupled with a fluorescent diethyl-amino-coumarin was able to maintain properties of cellular penetration on human cells. Here, we show that this property can be extended to the crossing of the Toxoplasma gondii cystic cell wall and the cell membrane of the parasite in its bradyzoite form, while maintaining a high efficacy as a histone deacetylase inhibitor. The investigation by molecular modeling allows a better understanding of the penetration mechanism.

Mechanistic Perspectives in the Regioselective Indole Addition to Unsymmetrical Silyloxyallyl Cations.

Our investigations on the reaction mechanism to account for regioselectivity on the addition of indoles to unsymmetrical silyloxyallyl cations are reported. Using both experimental and computational methods, we confirmed the significance of steric effects from the silyl ether group toward directing the inward approach of indoles, leading to nucleophilic attack at the less substituted electrophilic α'-carbon. The role of residual water toward accelerating the rate of reaction is established through stabilization of the participating silyloxyallyl cation.

Ion Pairing in HCl-Water Clusters: From Electronic Structure Investigations to Multiconfigurational Force-Field Development.

In the bulk, condensed-phase HCl exists as a dissociated Cl- ion and a proton that is delocalized over solvating water molecules. However, in the gas phase, HCl is covalent, and even on the introduction of hydrating water molecules, the HCl covalent state dominates small clusters and is relevant at larger clusters including 21 water molecules. Electronic structure calculations (at the MP2 level) and ab initio metadynamics simulations (at the DFT level) have been carried out on HCl-(H2O)n clusters with n = 2-22 to investigate distinct solvation environments in clusters from covalent HCl structure, to contact ion pairs and solvent-separated ion pairs. The data were further used to train and validate a multiconfigurational force-field for HCl-water clusters that incorporates covalent HCl states into the MS-EVB3.2 formalism. Additionally, the many-body interaction of the Cl- ion with water and the excess proton was modeled by the introduction of two geometric three-body terms that incorporates the dominant many-body interaction in an efficient noniterative manner.

Kinetic resolution in the [2+2] cycloaddition of ketenes: an experimental and theoretical study.

The kinetic resolution of Z and E olefins by [2+2] cycloaddition with ketenes allows the isolation of pure E olefin, as well as the synthesis of pure cis-cyclobutanones, starting from Z/E mixtures. A computational rationale for this kinetic difference is reported. The obtained difference of energy of activation matches with the experimental results.

Chemically and electrochemically triggered assembly of viologen radicals: towards multiaddressable molecular switches.

We have established that bipyridinium radicals can be reversibly π-dimerized under the combined effects of chemical (proton transfer) and electrochemical (electron transfer) stimuli. Our investigations also led to the discovery that a bis-pyridinyl appended calixarene intermediate is involved in a fully reversible redox-triggered σ-dimerization process. The structure of the most stable intramolecular σ-dimer was provided by computational chemistry and its complete conversion into a noncovalent π-dimer could be triggered chemically by addition of protons, leading to the formation of protonated cation radicals. Theoretical data collected with the N-methylated and N-protonated π-dimers also support the existence of multivariant orientations in π-bonded dimers of viologen cation-radicals.

Experimental and computational insights into carbon dioxide fixation by RZnOH species.

Organozinc hydroxides, RZnOH, possessing the proton-reactive alkylzinc group and the CO2 -reactive Zn-OH group, represent an intriguing group of organometallic precursors for the synthesis of novel zinc carbonates. Comprehensive experimental and computational investigations on 1) solution and solid-state behavior of tBuZnOH (1) species in the presence of Lewis bases, namely, THF and 4-methylpyridine; 2) step-by-step sequence of the reaction between 1 and CO2; and 3) the effect of a donor ligand and/or an excess of tBu2Zn as an external proton acceptor on the reaction course are reported. DFT calculations for the insertion of carbon dioxide into the dinuclear alkylzinc hydroxide 12 are fully consistent with (1)H NMR spectroscopy studies and indicate that this process is a multistep reaction, in which the insertion of CO2 seems to be the rate-determining step. Moreover, DFT studies show that the mechanism of the rearrangement between key intermediates, that is, the primary alkylzinc bicarbonate with a proximal position of hydrogen and the secondary alkylzinc bicarbonate with a distal position of hydrogen, most likely proceeds through internal rotation of the dinuclear bicarbonate.

Conformational flexibility of human casein kinase catalytic subunit explored by metadynamics.

Casein kinase CK2 is an essential enzyme in higher organisms, catalyzing the transfer of the γ phosphate from ATP to serine and threonine residues on protein substrates. In a number of animal tumors, CK2 activity has been shown to escape normal cellular control, making it a potential target for cancer therapy. Several crystal structures of human CK2 have been published with different conformations for the CK2α catalytic subunit. This variability reflects a high flexibility for two regions of CK2α: the interdomain hinge region, and the glycine-rich loop (p-loop). Here, we present a computational study simulating the equilibrium between three conformations involving these regions. Simulations were performed using well-tempered metadynamics combined with a path collective variables approach. This provides a reference pathway describing the conformational changes being studied, based on analysis of free energy surfaces. The free energies of the three conformations were found to be close and the paths proposed had low activation barriers. Our results indicate that these conformations can exist in water. This information should be useful when designing inhibitors specific to one conformation.

Investigation of binding-site homology between mushroom and bacterial tyrosinases by using aurones as effectors.

Tyrosinase is a copper-containing enzyme found in plants and bacteria, as well as in humans, where it is involved in the biosynthesis of melanin-type pigments. Tyrosinase inhibitors have attracted remarkable research interest as whitening agents in cosmetology, antibrowning agents in food chemistry, and as therapeutics. In this context, commercially available tyrosinase from mushroom (TyM) is frequently used for the identification of inhibitors. This and bacterial tyrosinase (TyB) have been the subjects of intense biochemical and structural studies, including X-ray diffraction analysis, and this has led to the identification of structural homology and divergence among enzymes from different sources. To better understand the behavior of potential inhibitors of TyM and TyB, we selected the aurone family-previously identified as potential inhibitors of melanin biosynthesis in human melanocytes. In this study, a series of 24 aurones with different hydroxylation patterns at the A- and B-rings were evaluated on TyM and TyB. The results show that, depending on the hydroxylation pattern of A- and B-rings, aurones can behave as inhibitors, substrates, and activators of both enzymes. Computational analysis was performed to identify residues surrounding the aurones in the active sites of both enzymes and to rationalize the interactions. Our results highlight similarities and divergence in the behavior of TyM and TyB toward the same set of molecules.

α-Halogenoacetanilides as hydrogen-bonding organocatalysts that activate carbonyl bonds: fluorine versus chlorine and bromine.

α-Halogenoacetanilides (X=F, Cl, Br) were examined as H-bonding organocatalysts designed for the double activation of CO bonds through NH and CH donor groups. Depending on the halide substituents, the double H-bond involved a nonconventional CH⋅⋅⋅O interaction with either a HCXn (n=1-2, X=Cl, Br) or a HCAr bond (X=F), as shown in the solid-state crystal structures and by molecular modeling. In addition, the catalytic properties of α-halogenoacetanilides were evaluated in the ring-opening polymerization of lactide, in the presence of a tertiary amine as cocatalyst. The α-dichloro- and α-dibromoacetanilides containing electron-deficient aromatic groups afforded the most attractive double H-bonding properties towards CO bonds, with a NH⋅⋅⋅O⋅⋅⋅HCX2 interaction.

The Pauson-Khand mechanism revisited: origin of CO in the final product.

The mechanism of the Pauson-Khand reaction has been studied by mass spectrometry and it has been found, through ion-molecule reaction with (13) CO, that the carbon monoxide incorporated into the product cyclopentenone is one that has been retained within the complex. Theoretical and kinetic calculations support this finding, which provides a complementary explanation for the effect of Pauson-Khand promoters.

Redox control of molecular motions in bipyridinium appended calixarenes.

A series of redox-responsive architectures featuring two bipyridinium units introduced onto the lower rim of a calixarene skeleton has been synthesized. The redox-triggered intramolecular dimerization of the reduced bipyridiniums has been investigated by electrochemistry, spectroelectrochemistry and by theoretical chemistry. The spectroscopic signature of the intramolecular dimers was found to evolve significantly with the size of the alkyl linker introduced between the calixarene skeleton and the bipyridinium units. On account of experimental data supported by theoretical calculations, these differences have been attributed to the extent of the orbital overlap in the π-dimerized species, involving either four or only two of the pyridine rings of the bipyridinium radical cations stacked in eclipsed or staggered conformations, respectively.

Redox control of rotary motions in ferrocene-based elemental ball bearings.

Rotational motions of ferrocene-based carousels have been achieved by electron transfer centered on π-dimerizable 4,4'-bipyridinium substituents introduced on both cyclopentadienyl rings through covalent linkers of different size, geometry, and flexibility. Detailed spectroscopic, electrochemical, and theoretical analyses demonstrate that rigid and fully conjugated linkers allow the quantitative formation of intramolecular π-dimers resulting from optimized orbital overlaps within the HOMO of the electrochemically generated bis-radical species. The tetra-cationic "charge-repelled" conformers, the self-assembled π-dimers, and their electron triggered interconversions have been investigated by UV-vis, NMR, and ESR spectroscopy, electrochemistry, X-ray diffraction analysis, and theoretical calculations. These studies support the conclusion that the rotation of both cyclopentadienyl rings in ferrocene can be controlled electrochemically using noncovalent reversible interactions arising from π-radical coupling processes.

Did Homocysteine Take Part in the Start of the Synthesis of Peptides on the Early Earth?

Unlike its shorter analog, cysteine, and its methylated derivative, methionine, homocysteine is not today a proteinogenic amino acid. However, this thiol containing amino acid is capable of forming an activated species intramolecularly. Its thiolactone could have made it an interesting molecular building block at the origin of life on Earth. Here we study the cyclization of homocysteine in water and show theoretically and experimentally that in an acidic medium the proportion of thiolactone is significant. This thiolactone easily reacts with amino acids to form dipeptides. We envision that these reactions may help interpret why a methionine residue is introduced at the start of all protein synthesis.

A way to thioacetate esters compatible with non-oxidative prebiotic conditions.

The centrality of pyruvate oxidative decarboxylation into acetyl-CoA in current biochemistry is a strong argument for proposing that a similar reaction have been necessary for the development of an effective protometabolism on the primitive Earth. However, such a decarboxylation requires the use of an oxidant and a catalyst, today enzymatic. Based on the mechanisms of the pyruvate dehydrogenase complex and pyruvate-ferredoxin oxidoreductase, we propose that the initial mechanism involved disulfides and occurred via radicals. A first disulfide is obtained by reacting glyoxylate with hydrogen sulfide. It is then possible to produce a wide variety of other disulfides by exchange reactions. When reacted with pyruvate under UV light they give thioesters. This process requires no oxidant and is therefore compatible with what is known of the redox conditions of the early Earth. Neither does it require any catalyst. It could be the first way to acetyl thioesters, a way that was later improved by the introduction of catalysts, first minerals, then enzymes.

Interfacial Water at Graphene Oxide Surface: Ordered or Disordered?

The graphene oxide (GO)-water interface was simulated using Born-Oppenheimer molecular dynamics (BOMD) simulations with two different functionals, namely, revPBE-D3 and BLYP-D2, as well as a commonly used classical force field, namely, OPLS-AA. A number of different order parameters, including the orientation of the interfacial water molecules near the aromatic region of the GO surface as well as those near the oxygenated defects, were examined and compared. The BOMD interfacial waters are clearly much less structured as compared to the classical force field that shows a strongly ordered interface. Higher-level calculations, namely, symmetry adapted perturbation theory, were performed on representative clusters taken from the BOMD simulation. These calculations revealed not only that a number of conformations have similar interaction energies but also the importance of induction contribution to the interaction energies.

Synthesis of N-acridinyl-N'-alkylguanidines: dramatic influence of amine to guanidine replacement on the physicochemical properties.

Transformation of aminoacridines into N-acridinyl-N'-alkylguanidines is described. The chosen procedure allows introduction of pendent substituents (exemplified by N,N-dimethylaminopropyl chain) into key acridinyl thioureas, thus opening the way to structural diversity. Spectroscopic study and pK(a) determination show that the presence of the strongly basic guanidine has a dramatic influence on the ionization of the acridine nucleus by lowering the pk(a) value down to 4.49.

The Reaction of Aminonitriles with Aminothiols: A Way to Thiol-Containing Peptides and Nitrogen Heterocycles in the Primitive Earth Ocean.

The Strecker reaction of aldehydes with ammonia and hydrogen cyanide first leads to α-aminonitriles, which are then hydrolyzed to α-amino acids. However, before reacting with water, these aminonitriles can be trapped by aminothiols, such as cysteine or homocysteine, to give 5- or 6-membered ring heterocycles, which in turn are hydrolyzed to dipeptides. We propose that this two-step process enabled the formation of thiol-containing dipeptides in the primitive ocean. These small peptides are able to promote the formation of other peptide bonds and of heterocyclic molecules. Theoretical calculations support our experimental results. They predict that α-aminonitriles should be more reactive than other nitriles, and that imidazoles should be formed from transiently formed amidinonitriles. Overall, this set of reactions delineates a possible early stage of the development of organic chemistry, hence of life, on Earth dominated by nitriles and thiol-rich peptides (TRP).

Bond dissociation energies of carbonyl gold complexes: a new descriptor of ligand effects in gold(i) complexes?

Ligand electronic effects in gold(i) chemistry have been evaluated by means of the experimental determination of M-CO bond dissociation energies for 16 [L-Au-CO]+ complexes, bearing L ligands widely used in gold catalysis. Energy-resolved analyses have been made using tandem mass spectrometry with collision-induced dissociation. Coupled with DFT calculations, this approach enables the quantification of ligand effects based on the LAu-CO bond strength. A further energy decomposition analysis gives access to detailed insights into this bond's characteristics. Whereas small differences are observed between phosphine- and phosphite-containing gold complexes, carbene ligands are shown to stabilize the gold-carbonyl bond much more efficiently.