One- and Two-Electron Reductions in MiniSOG and their Implication in Catalysis.

The unconventional bioorthogonal catalytic activation of anticancer metal complexes by flavin and flavoproteins photocatalysis has been reported recently. The reactivity is based on a two-electron redox reaction of the photoactivated flavin. Furthermore, when it comes to flavoproteins, we recently reported that site mutagenesis can modulate and improve this catalytic activity in the mini Singlet Oxygen Generator protein (SOG). In this paper, we analyze the reductive half-reaction in different miniSOG environments by means of density functional theory. We report that the redox properties of flavin and the resulting reactivity of miniSOG is modulated by specific mutations, which is in line with the experimental results in the literature. This modulation can be attributed to the fundamental physicochemical properties of the system, specifically (i) the competition of single and double reduction of the flavin and (ii) the probability of electron transfer from the protein to the flavin. These factors are ultimately linked to the stability of flavin's electron-accepting orbitals in different coordination modes.

Enhancing the Photocatalytic Conversion of Pt(IV) Substrates by Flavoprotein Engineering.

Our recent work demonstrates that certain flavoproteins can catalyze the redox activation of Pt(IV) prodrug complexes under light irradiation. Herein, we used site-directed mutagenesis on the mini singlet oxygen generator (mSOG) to modulate the photocatalytic activity of this flavoprotein toward two model Pt(IV) substrates. Among the prepared mutants, Q103V mSOG displayed enhanced catalytic efficiency as a result of its longer triplet excited-state lifetime. This study shows, for the first time, that protein engineering can improve the catalytic capacity of a protein toward metal-containing substrates.

Theoretical characterization of Al(III) binding to KSPVPKSPVEEKG: Insights into the propensity of aluminum to interact with key sequences for neurofilament formation.

Classical molecular dynamic simulations and density functional theory are used to unveil the interaction of aluminum with various phosphorylated derivatives of the fragment KSPVPKSPVEEKG (NF13), a major multiphosphorylation domain of human neurofilament medium (NFM). Our calculations reveal the rich coordination chemistry of the resultant structures with a clear tendency of aluminum to form multidentate structures, acting as a bridging agent between different sidechains and altering the local secondary structure around the binding site. Our evaluation of binding energies allows us to determine that phosphorylation has an increase in the affinity of these peptides towards aluminum, although the interaction is not as strong as well-known chelators of aluminum in biological systems. Finally, the presence of hydroxides in the first solvation layer has a clear damping effect on the binding affinities. Our results help in elucidating the potential structures than can be formed between this exogenous neurotoxic metal and key sequences for the formation of neurofilament tangles, which are behind of some of the most important degenerative diseases.

Tetravalent Oxygen and Sulphur Centres Mediated by Carborane Superacid: Theoretical Analysis.

The tetravalent oxygen or sulphur centres, especially in H4 O2+ and H4 S2+ dications, were analysed experimentally and theoretically in various studies. Herein, we discuss stabilities of such centres in related H(CH3 )3 O2+ and H(CH3 )3 S2+ dications mediated by carborane superacid. The ωB97X-D/6-311++G(d,p) calculations were performed for a gas phase and for different solvents characterized by a wide range of dielectric constants for complexes of these dications with the conjugated base of H(CHB11 F11 ) carborane superacid, CHB11 F11- , which indicate that these complexes are linked by hydrogen bonds. The Quantum Theory of 'Atoms in Molecules' (QTAIM) approach is applied to characterize these interactions. DFT results show that tetravalent oxygen and sulphur structures are additionally stabilized by polar solvents.

Does phosphorylation increase the binding affinity of aluminum? A computational study on the aluminum interaction with serine and O-phosphoserine.

Several toxic effects arise from aluminum's presence in living systems, one of these effects is to alter the natural role of enzymes and non-enzyme proteins. Aluminum promotes the hyperphosphorylation of normal proteins. In order to assess the aluminum-binding abilities of phosphorylated proteins and peptides, the interaction of aluminum at different pH with serine and phosphoserine is studied by a Density Functional Theory study, combined with polarizable continuum models to account for bulk solvent effects, and the electronic structure of selected complexes are analyzed by Quantum Theory of "Atoms in Molecules". Our results confirm the high ability of aluminum to bind polypeptides as the pH lowers. Moreover, the phosphorylation of the building blocks increases the affinity for aluminum, in particular at physiological pH. Finally, aluminum shows a tendency to be chelated forming different size rings.

Tuning the affinity of catechols and salicylic acids towards Al(iii): characterization of Al-chelator interactions.

Due to aluminum's controversial role in neurotoxicity, the goal of chelation therapy, the removal of the toxic metal ion or attenuation of its toxicity by transforming it into less toxic compounds, has attracted considerable interest in the past years. In the present paper we present, validate and apply a state-of-the-art theoretical protocol suitable for the characterization of the interactions between a chelating agent and Al(iii). In particular, we employ a cluster-continuum approach based on Density Functional Theory calculations to evaluate the binding affinity of aluminum for a set of two important families of aromatic chelators: salicylic acids and catechols. Our protocol shows very good qualitative agreement between the computed binding affinities and available experimental stability constants (log ß) values for 1 : 1, 1 : 2 and 1 : 3 complexes. Then, we have investigated the nature of the Al-O bond in an enlarged dataset of 27 complexes of 1 : 1 stoichiometry, by means of the QTAIM and Energy Decomposition Analysis (EDA). Quite interestingly, we have found that although the Al-O interaction is mainly electrostatic, there is a small but significant degree of covalency that explains the modulation of binding affinities in both families of compounds by the addition of electron donating (CH3, OCH3) or withdrawing (NO2, CF3) substituents. The role of aromaticity and the mechanisms of action of the different functional groups were also evaluated. Finally, we have analyzed the competition between Al(iii) and proton toward the binding of these chelators, giving a rationalization of the different trends found experimentally between log ß and the amount of free aluminum in solution in the presence of a given ligand (p[Al]). In summary, we propose a validated and comprehensive computational protocol that can provide a valuable help toward the design and tuning of new efficient aluminum chelators.

The role of non-covalent interactions in the self-healing mechanism of disulfide-based polymers.

In this work, a theoretical protocol based on classical molecular dynamics has been defined, in order to study weak non-covalent interactions in diphenyl disulfide based compounds. This protocol is then used to study the influence of hydrogen bonds and π-π stacking in four selected cases, namely, monosubstituted and amine ortho trisubstituted urea and urethane-based diphenyl disulfides. In all cases, it has been observed that hydrogen bonds are much more relevant than π-π stacking, which has little influence. In addition, hydrogen bonds are the responsible to maintain the polymeric chains close, so that the disulfides may reach the reacting region, even in urethane-based materials, where the lower amount of hydrogen bonds formed make the chains more flexible and mobile. Combining the results obtained by classical molecular dynamics with those obtained earlier by means of quantum mechanics, we conclude that there are two main factors that are relevant to the self-healing properties of disulfide-based materials: firstly, the capacity to generate sulfenyl radicals by breaking the disulfide S-S bond and, secondly, the ability of these radicals to attack neighboring disulfides. The former is dominated by the bond dissociation energy of the S-S bond, while the latter is strongly influenced by two other factors. On the one hand, the hydrogen bonding interactions established between chains, and on the other, the energy barriers for the attack of sulfur radicals to neighbor disulfides. We have defined three new parameters to estimate the influence of these features, with the aim of predicting the self-healing capacity of disulfides and related materials, which will help experimentalists in the development of improved materials.

Structural and optical properties of the naked and passivated Al5Au5 bimetallic nanoclusters.

The structural and optical properties of both the naked and passivated bimetallic Al5Au5 nanoclusters have been analyzed based on data obtained from ab initio density functional theory and quantum molecular dynamics simulations. It has been found that the Al5Au5 nanocluster possesses a hollow shaped minimum energy structure with segregated Al and Au layered domains, the former representing the electrophilic domain and the latter the nucleophilic domain. In particular, it has been shown that alkali metal cations attach in the nucleophilic domain and hop from one Au site to the next one in the picoseconds time scale, while anions are bound tightly to the Al atoms of the electrophilic domain. Simulating annealing studies are very suggestive of the proneness of the nanocluster towards coalescence into large cluster units, when the cluster is left unprotected by appropriate ligands. Further passivation studies with NaF salt suggest, nonetheless, the possibility of the isolation of the Al5Au5 cluster in molten salts or ionic liquids.

Phosphorylation promotes Al(iii) binding to proteins: GEGEGSGG as a case study.

Aluminum, the third most abundant element in the Earth's crust and one of the key industrial components of our everyday life, has been associated with several neurodegenerative diseases due to its ability to promote neurofilament tangles and ß-amyloid peptide aggregation. However, the experimental characterization of aluminum speciation in vivo is a difficult task. In the present study, we develop a theoretical protocol that combines molecular dynamics simulations, clustering of structures, and density functional theory for the characterization of the binding of aluminum to the synthetic neurofilament analogue octapeptide GEGEGSGG and its phosphorylated variant. Our protocol is tested with respect to previous NMR experimental data, which allows for a full interpretation of the experimental information available and its relationship with key thermodynamic quantities. Our results demonstrate the importance of phosphorylation in the ability of a peptide to bind to aluminum. Thus, phosphorylation: (i) changes the binding pattern of aluminum to GEGEGSGG, shifting the preferential binding site from the C-terminal to S6(P); (ii) increases the binding affinity by a factor of around 15 kcal mol(-1) in free energy; and (iii) may cause significant changes in the secondary structure and stiffness of the polypeptide chain, specially in the case of bidentate binding modes. Our results shed light on the possibility of aluminum to induce aggregation of ß-amyloid proteins and neurofilament tangles.

Aluminum and its effect in the equilibrium between folded/unfolded conformation of NADH.

Nicotinamide adenine dinucleotide (NADH) is one of the most abundant cofactor employed by proteins and enzymes. The molecule is formed by two nucleotides that can lead to two main conformations: folded/closed and unfolded/open. Experimentally, it has been determined that the closed form is about 2 kcal/mol more stable than the open formed. Computationally, a correct description of the NADH unfolding process is challenging due to different reasons: 1) The unfolding process shows a very low energy difference between the two conformations 2) The molecule can form a high number of internal hydrogen bond interactions 3) Subtle effects such as dispersion may be important. In order to tackle all these effects, we have employed a number of different state of the art computational techniques, including: a) well-tempered metadynamics, b) geometry optimizations, and c) Quantum Theory of Atoms in Molecules (QTAIM) calculations, to investigate the conformational change of NADH in solution and interacting with aluminum. All the results indicate that aluminum indeed favors the closed conformation of NADH, due mainly to the formation of a more rigid structure through key hydrogen bond interactions.

Energetics and structural characterization of the large-scale functional motion of adenylate kinase.

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.

Magnetic endohedral transition-metal-doped semiconducting-nanoclusters.

Endohedral first-row transition-metal-doped TM@Zn(i)S(i) nanoclusters, in which TM stands for the first-row transition-metals from Sc to Zn, and i=12, 16, have been characterized. In these structures the dopant metals are trapped inside spheroidal hollow semiconducting nanoclusters. It is observed that some of the transition metals are trapped in the center of mass of the cluster, whereas others are found to be displaced from that center, leading to structures in which the transition metals display a complex dynamical behavior upon encapsulation. This fact was confirmed by quantum molecular dynamics calculations, which further confirmed the thermal stability of endohedral compounds. In the endohedrally-doped nanoclusters in which the transition-metal atom sits on the center of mass, the host hollow cluster structure remains undistorted after dopant encapsulation. Conversely, if the encapsulated transition-metal atom is displaced from the center of mass, the host hollow cluster structure suffers a very tiny distortion. Additionally, it is found that there is negligible charge transfer between the dopant transition-metal atom and its hollow cluster host and, after encapsulation, the spin densities remain localized on the transition-metal atom. This allows for the atomic-like behavior of the trapped transition-metal atom, which gives rise to their atomic-like magnetic properties. The encapsulation free energies are negative, suggesting that these compounds are thermodynamically stable.

Reaction mechanism of the acidic hydrolysis of highly twisted amides: Rate acceleration caused by the twist of the amide bond.

We present an ab initio study of the acid hydrolysis of a highly twisted amide and a planar amide analogue. The aim of these studies is to investigate the effect that the twist of the amide bond has on the reaction barriers and mechanism of acid hydrolysis. Concerted and stepwise mechanisms were investigated using density functional theory and polarizable continuum model calculations. Remarkable differences were observed between the mechanism of twisted and planar amide, due mainly to the preference for N-protonation of the former and O-protonation of the latter. In addition, we were also able to determine that the hydrolytic mechanism of the twisted amide will be pH dependent. Thus, there is a preference for a stepwise mechanism with formation of an intermediate in the acid hydrolysis, whereas the neutral hydrolysis undergoes a concerted-type mechanism. There is a nice agreement between the characterized intermediate and available X-ray data and a good agreement with the kinetically estimated rate acceleration of hydrolysis with respect to analogous undistorted amide compounds. This work, along with previous ab initio calculations, describes a complex and rich chemistry for the hydrolysis of highly twisted amides as a function of pH. The theoretical data provided will allow for a better understanding of the available kinetic data of the rate acceleration of amides upon twisting and the relation of the observed rate acceleration with intrinsic differential reactivity upon loss of amide bond resonance.

Sandwich complexes based on the "all-metal" Al4 2- aromatic ring.

We report on novel sandwichlike structures [Al(4)MAl(4)](q-) (q=0-2 and M=Ti, V, Cr, Zr, Nb, Mo, Hf, Ta and W) based on the recently synthesized all-metal aromatic Al(4)(2-) square ring. The sandwichlike structures have two aromatic tetraaluminum square rings which trap a transition-metal cation from either the first, second, or third row. The stability of the anionic sandwichlike complexes towards electron detachment is discussed, and addition of alkali cations is found to stabilize the 2- charged complexes, preventing spontaneous electron detachment. Once the sandwichlike complexes are formed, the Al(4)(2-) square properties remain nearly unchanged; this fact strongly supports the hypothesis that in these complexes the Al(4)(2-) square rings remain aromatic.