Exploring the Esterase Catalytic Activity of Minimalist Heptapeptide Amyloid Fibers.

This paper investigates the esterase activity of minimalist amyloid fibers composed of short seven-residue peptides, IHIHIHI (IH7) and IHIHIQI (IH7Q), with a particular focus on the role of the sixth residue position within the peptide sequence. Through computational simulations and analyses, we explore the molecular mechanisms underlying catalysis in these amyloid-based enzymes. Contrary to initial hypotheses, our study reveals that the twist angle of the fiber, and thus the catalytic site's environment, is not notably affected by the sixth residue. Instead, the sixth residue interacts with the p-nitrophenylacetate (pNPA) substrate, particularly through its -NO2 group, potentially enhancing catalysis. Quantum mechanics/molecular mechanics (QM/MM) simulations of the reaction mechanism suggest that the polarizing effect of glutamine enhances catalytic activity by forming a stabilizing network of hydrogen bonds with pNPA, leading to lower energy barriers and a more exergonic reaction. Our findings provide valuable insights into the intricate interplay between peptide sequence, structural arrangement, and catalytic function in amyloid-based enzymes, offering potentially valuable information for the design and optimization of biomimetic catalysts.

Canonical, deprotonated, or zwitterionic? II. A computational study on amino acid interaction with the TiO2(110) rutile surface: comparison with the anatase (101) surface.

The adsorption of 11 amino acids (Gly, Leu, Met, Phe, Ser, Cys, Glu, Gln, Arg, Lys, and His) on the TiO2(110) rutile surface is investigated adopting a theoretical approach, using the PBE-D2* functional as implemented in the periodic VASP code. The adsorption of the amino acids is considered in their canonical, deprotonated and zwitterionic forms. For all cases, the most stable adsorption mode adopts a bidentate (O,O) binding with surface undercoordinated Ti atoms, in agreement with previous experimental and computational studies using glycine as a test case. Such a binding mode is possible due to the surface morphology, because the Ti-Ti distances match very well with the carboxylic O-O distance. The most stable adsorption states are the deprotonated and the zwitterionic ones, the canonical one lying significantly above in energy. The relative stability between the deprotonated and the zwitterionic states results in a delicate trade-off among dative interactions (O, N, and S atoms of the amino acids with Ti atoms of the surface), H-bond interactions, dispersive forces and, to a lesser extent, steric hindrance of the amino acidic lateral chains. Finally, the difference in the amino acid adsorption between the (110) rutile and the (101) anatase surfaces is discussed both from the energetic and surface morphological standpoints, highlighting the larger reactivity of the rutile polymorph in adsorbing and deprotonating the amino acids compared with the anatase one.

Site-selective-induced isomerization of formamide.

The new capacity of X-ray free-electron laser (XFEL) facilities to produce multi-color X-ray femtosecond pulses paves the way to explore ultrafast phenomena in matter induced by X-ray photons. In the present study, we exploit the site-selectivity and the high temporal resolution of a two-color X-ray femtosecond pump-probe sequence to investigate the isomerization of formamide. The pump pulse excites a particular atomic site in the molecule, while the probe pulse captures changes in the chemical environment at a remote atomic site. The response of the system is found to strongly depend on the nature of the excited site, and the core excitation provides selective control over chemical bond breaking. In particular, we show that the N1s → π* transition can induce the isomerization reaction in formamide and demonstrate the possibility to observe in real time hydrogen migration by measuring the chemical shifts with the X-ray probe pulse. This work opens a unique prospect for X-ray-induced photochemistry at XFEL facilities.

Reactivity of Metal Carbenes with Olefins: Theoretical Insights on the Carbene Electronic Structure and Cyclopropanation Reaction Mechanism.

Present work addresses the reactivity of several phenyl-substituted metal-carbene complexes with 4-methylstyrene by means of density functional theory OPBE simulations. Different paths that lead to cyclopropanation were explored and compared to the olefin metathesis mechanism. For this purpose, we chose four different catalysts: (i) the Grubbs second-generation olefin metathesis catalyst, (ii) a Grubs second-generation-like complex, in which ruthenium is replaced by iron, and (iii) two iron carbene complexes (a piano stool and a porphyrin iron carbene) that experimentally catalyze alkene cyclopropanation. Results suggest that the nature of the applying mechanism is very sensitive to the coordination around the metal center and the spin state of the metal-carbene complex. Cyclopropanation by open-shell metal-carbene complexes seems to preferentially proceed through a two-step radical mechanism, in which the two C-C bonds are sequentially formed (path C). Singlet-state carbenes proceed either through a direct attack of the olefin to the carbene (path D) when the formation of the metallacycle is not feasible or through a reductive elimination from the metallacyclobutane when this intermediate is accessible both kinetically and thermodynamically (path B).

[2 + 2] Photocycloaddition of 2(5H)-furanone to unsaturated compounds. insights from first principles calculations and transient-absorption measurements.

The [2 + 2] photocycloaddition reaction of 2(5H)-furanone to ethylene and acetylene has been investigated by means of DFT and CASSCF methods. In both cases, the reaction involves the formation of a triplet 1,4-biradical intermediate that evolves to the cyclobutane product after spin inversion. For acetylene, the lowest energy path in the triplet surface occurs through the (3)(pi-pi*) state of the 2(5H)-furanone. However, in the reaction with ethylene the lowest energy path in the triplet surface involves the (3)(pi-pi*) state of the alkene. Although reaction through the triplet state of olefins is usually disregarded due to the short lifetime of these species, we have experimentally measured that sensitization of ethylene triplet state can occur at typical synthetic conditions and, thus, lead to photochemical addition to the lactone.

Coordination properties of lysine interacting with Co(I) and Co(II). A theoretical and mass spectrometry study.

This article analyzes the interaction between cobalt cations and lysine both theoretically and experimentally. The influence of d orbital occupation in Co(+/2+) cations and the side chain of lysine on the relative stability of the different coordination modes was studied by means of theoretical methods. The structure and vibrational frequencies were determined using the B3LYP and BHLYP methods. Single-point calculations were also carried out at the CCSD(T) level. For both systems, Co+-lysine and Co2+-lysine, the most stable structure results from the interaction of neutral lysine to the metal cation through the two amino groups and the carbonyl oxygen, the ground electronic state being a 3A in the case of Co+ and 4A for the Co2+ system. This is in contrast to that found for Co2+ interacting with glycine in which the most stable structure has the amino acid in its zwitterionic form, which points out the importance of the side chain.

Is the peptide bond formation activated by Cu(2+) interactions? Insights from density functional calculations.

The catalytic role that Cu(2+) cations play in the peptide bond formation has been addressed by means of density functional calculations. First, the Cu(2+)-(glycine)2 --> Cu(2+)-(glycylglycine) + H2O reaction was investigated since mass spectrometry low collision activated dissociation (CAD) spectra of Cu(2+)-(glycine)2 led to the elimination of a water molecule, which suggested that an intracomplex peptide bond formation might have occurred. Results show that this intracomplex condensation is associated to a very high free energy barrier (97 kcal mol(-1)) and reaction free energy (66 kcal mol(-1)) because of the loss of metal coordination during the reaction. Second, on the basis of the salt-induced peptide formation theory, the condensation reaction between two glycines was studied in aqueous solution using discrete water molecules and the conductor polarized continuum model (CPCM) continuous method. It is found that the synergy between the interaction of glycines with Cu(2+) and the presence of water molecules acting as proton-transfer helpers significantly lower the activation barrier (from 55 kcal/mol for the uncatalyzed system to 20 kcal/mol for the Cu(2+) solvated system) which largely favors the formation of the peptide bond.

Effects of ionization, metal cationization and protonation on 2'-deoxyguanosine: changes on sugar puckering and stability of the N-glycosidic bond.

The influence of oxidation, protonation, and metal cationization with Cu(+) and Cu(2+) on the strength of the N-glycosidic bond in 2'-deoxyguanosine has been studied by means of quantum chemical calculations. In all cases, the N9-C1' bond distance increases (0.03-0.06 A) upon introducing positive charge in the guanine moiety, the observed variations being more important for the dicationic systems. Binding energies show that the effect of X(n)(+) in guanine hinders the homolytic dissociation, whereas it largely favors the heterolytic process. With respect to the deoxyribose ring, it has been found that metal binding, oxidation, and protonation do not significantly change the values of the phase angle of pseudorotation P. However, the glycosyl torsion angle chi varies considerably (from 242.0 degrees to 189.8 degrees) as a consequence of a stabilizing guanine-sugar (H8-O4') interaction due to the increase of acidity of guanine C8-H8 upon cationization.

Does Fe(2+) in olivine-based interstellar grains play any role in the formation of H2? Atomistic insights from DFT periodic simulations.

Using periodic DFT-D2 methods, atomistic simulations of interstellar H adsorption and H2 formation on a (010) Fe-containing olivine surface are presented. At variance with the (010) Mg2SiO4 surface and key to these processes are the large Fe/H interaction energies, suggesting that olivine surfaces are good reservoirs of H atoms for subsequent recombination to form H2.

Thioflavin-based molecular probes for application in Alzheimer's disease: from in silico to in vitro models.

Alzheimer's disease (AD) is a neurological disease of confusing causation with no cure or prevention available. The definitive diagnosis is made postmortem, in part through the presence of amyloid-beta plaques in the brain tissue, which can be done with the small molecule thioflavin-T (ThT). Plaques are also found to contain elevated amounts of metal ions Cu(ii) and Zn(ii) that contribute to the neurotoxicity of amyloid-beta (Aß). In this paper, we report in silico, in vitro, and ex vivo studies with ThT-derived metal binders 2-(2-hydroxyphenyl)benzoxazole (HBX), 2-(2-hydroxyphenyl)benzothiazole (HBT) and their respective iodinated counterparts, HBXI and HBTI. They exhibit low cytotoxicity in a neuronal cell line, potential blood-brain barrier penetration, and interaction with Aß fibrils from senile plaques present in human and transgenic mice AD models. Molecular modelling studies have also been undertaken to understand the prospective ligand-Aß complexes as well as to rationalize the experimental findings. Overall, our studies demonstrate that HBX, HBT, HBXI, and HBTI are excellent agents for future use in in vivo models of AD, as they show in vitro efficacy and biological compatibility. In addition to this, we present the glycosylated form of HBX (GBX), which has been prepared to take advantage of the benefits of the prodrug approach. Overall, the in vitro and ex vivo assays presented in this work validate the use of the proposed ThT-based drug candidate series as chemical tools for further in vivo development.

On the bonding of first-row transition metal cations to guanine and adenine nucleobases.

The binding of first-row transition metal monocations (Sc+-Cu+) to N7 of guanine and N7 or N3 of adenine nucleobases has been analyzed using the hybrid B3LYP density functional theory (DFT) method. The nature of the bonding is mainly electrostatic, the electronic ground state being mainly determined by metal-ligand repulsion. M+-guanine binding energies are 18-27 kcal/mol larger than those of M+-adenine, the difference decreasing along the row. Decomposition analysis shows that differences between guanine and adenine mainly arise from Pauli repulsion and the deformation terms, which are larger for adenine. Metal cation affinity values at this level of calculation are in very good agreement with experimental data obtained by Rodgers et al. (J. Am. Chem. Soc. 2002, 124, 2678) for adenine nucleobases.

Coordination properties of the oxime analogue of glycine to Cu(II).

The coordination of Cu2+ by glyoxilic acid oxime (gao)--the oxime analogue of glycine amino acid--and its deprotonated (gao- and gao2-) species has been studied with different density functional methods. Single-point calculations have also been carried out at the single- and double- (triple) excitation coupled-cluster (CCSD(T)) level of theory. The isomers studied involve coordination of Cu2+ to electron-rich sites (O,N) of neutral, anionic, and dianionic gao species in different conformations. In contrast to Cu2+-glycine, for which the ground-state structure is bidentate with the CO2(-) terminus of zwitterionic glycine, for Cu2+-gao the most stable isomer shows monodentate binding of Cu2+ with the carbonylic oxygen of the neutral form. The most stable complexes of Cu2+ interacting with deprotonated gao species (gao- and gao2-) also take place through the carboxylic oxygens but in a bidentate manner. The results with different functionals show that, for these open shell (Cu2+-L) systems, the relative stability of complexes with different coordination environments (and so, different spin distribution) can be quite sensitive to the amount of "Hartree-Fock" exchange included in the functional. Among all the functionals tested in this work, the BHandHLYP is the one that better compares to CCSD(T) results.

Interaction of Co+ and Co2+ with glycine. A theoretical study.

Cobalt cations are open shell systems with several possible electronic states arising from the different occupations of the 3d and 4s orbitals. The influence of these occupations on the relative stability of the coordination modes of the metal cation to glycine has been studied by means of theoretical methods. The structure and vibrational frequencies have been determined using the B3LYP method. Single-point calculations have also been carried out at the CCSD(T) level. The most stable structure of Co(+)-glycine is bidentate, with the Co(+) cation interacting with the amino group and the carbonyl oxygen of neutral glycine, and the ground electronic state being (3)A. For Co(2+)-glycine, the lowest energy structure corresponds to the interaction of the metal cation with the carboxylate group of the zwitterionic glycine, the ground electronic state being (4)A''.

Gas phase intramolecular proton transfer in cationized glycine and chlorine substituted derivatives (M-Gly, M = Na+, Mg2+, Cu+, Ni+, and Cu2+): existence of Zwitterionic structures?

The intramolecular proton transfer in cationized glycine and chlorine substituted derivatives with M = Na+, Mg2+, Ni+, Cu+, and Cu2+ has been studied with the three parameter B3LYP density functional method. The coordination of metal cations to the oxygens of the carboxylic group of glycine stabilizes the zwitterionic structure. For all monocations the intramolecular proton transfer occurs readily with small energy barriers (1-2 kcalmol(-1)). For the dication Mg2+ and Cu2+ systems, the zwitterionic structure becomes very stable. However, whereas for Mg2+, the proton transfer process takes place spontaneously, for Cu2+ the reaction occurs with an important energy barrier. The substitution of the hydrogens of the amino group by chlorine atoms decreases the basicity of nitrogen, which destabilizes the zwitterionic structure. For monosubstituted glycine complexed with Na+, the zwitterionic structure still exists as a minimum, but for disubstituted glycine no minimum appears for this structure. In contrast, for Mg2+ complexed to mono- and disubstituted glycine, the zwitterionic structure remains the only minimum, since the enhanced electrostatic interaction with the dication overcomes the destabilizing effect of the chlorine atoms.