Revisiting the reaction pathways for phospholipid hydrolysis catalyzed by phospholipase A2 with QM/MM methods.

Secreted phospholipase A2 (sPLA2) is a Ca2+-dependent, widely distributed enzyme superfamily in almost all mammalian tissues and bacteria. It is also a critical component of the venom of nearly all snakes, as well as many invertebrate species. In non-venomous contexts, sPLA2 assumes significance in cellular signaling pathways by binding cell membranes and catalyzing ester bond hydrolysis at the sn-2 position of phospholipids. Elevated levels of GIIA sPLA2 have been detected in the synovial fluid of arthritis patients, where it exhibits a pro-inflammatory function. Consequently, identifying sPLA2 inhibitors holds promise for creating highly effective pharmaceutical treatments. Beyond arthritis, the similarities among GIIA sPLA2s offer an opportunity for developing treatments against snakebite envenoming, the deadliest neglected tropical disease. Despite decades of study, the details of PLA2 membrane-binding, substrate-binding, and reaction mechanism remain elusive, demanding a comprehensive understanding of the sPLA2 catalytic mechanism. This study explores two reaction mechanism hypotheses, involving one or two water molecules, and distinct roles for the Ca2+ cofactor. Our research focuses on the human synovial sPLA2 enzyme bound to lipid bilayers of varying phospholipid compositions, and employing adiabatic QM/MM and QM/MM MD umbrella sampling methods to energetically and geometrically characterize the structures found along both reaction pathways. Our studies demonstrate the higher frequency of productive conformations within the single-water pathway, also revealing a lower free energy barrier for hydrolyzing POPC. Furthermore, we observe that the TS of this concerted one-step reaction closely resembles transition state geometries observed in X-ray crystallography complexes featuring high-affinity transition state analogue inhibitors.

Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules.

Graphene oxide (GO), a nanomaterial with promising applications that range from water purification to enzyme immobilization, is actively present in scientific research since its discovery. GO studies with computational methodologies such as molecular dynamics are frequently reported in the literature; however, the models used often rely on approximations, such as randomly placing functional groups and the use of generalized force fields. Therefore, it is important to develop new MD models that provide a more accurate description of GO structures and their interaction with an aqueous solvent and other adsorbate molecules. In this paper, we derived new force field non-bonded parameters from linear-scaling density functional theory calculations of nanoscale GO sheets with more than 10,000 atoms through an atoms-in-molecules (AIM) partitioning scheme. The resulting GAFF2-AIM force field, derived from the bonded terms of GAFF2 parameterization, reproduces the solvent structure reported in ab initio MD simulations better than the force field nowadays widely used in the literature. Additionally, we analyzed the effect of the ionic strength of the medium and of the C/O ratio on the distribution of charges surrounding the GO sheets. Finally, we simulated the adsorption of natural amino acid molecules to a GO sheet and estimated their free energy of binding, which compared very favorably to their respective experimental values, validating the force field presented in this work.

BN-Doped Graphene and Single-Walled Carbon Nanotubes for the Catalysis of SN2 Reactions: Insights from Density Functional Theory Modeling.

The inner space of carbon nanotubes has already been proven to provide a type of confinement, which can dramatically alter the energetics of chemical reactions when compared to the gas phase. Moreover, BN doping can be used to fine-tune electronic properties, which might influence the enthalpy and activation energy of chemical reactions that take place inside their inner space. The energy profile of the prototype Menshutkin SN2 reaction between ammonia and chloromethane has been analyzed in a variety of carbon-based materials at the DFT (density functional theory) level. Pristine zigzag (9,0) and (12,0) single-walled carbon nanotubes and graphene sheets have been doped with boron and nitrogen at different stoichiometries, namely, BN, BNC, BNC2, and BNC4, that resulted in remarkable variations of their catalytic effects. Graphene has revealed to be the support material, which depends less on doping in terms of enthalpy and energy barrier of the reaction. However, when graphene is rolled up into tubular forms, the influence of doping becomes increasingly stronger as the nanotube radius decreases. In the case of BNC4 doping of (9,0) nanotubes, the activation energy drops 10 kcal/mol when compared to the pristine case, and the reaction became even exothermic by more than 15 kcal/mol.

Biomimetic one-pot route to acridine epoxides.

The first direct epoxidation of acridine on the edge positions is reported. The reaction proceeds under mild conditions using a biomimetic catalytic system based on a Mn(III) porphyrin. The successive oxyfunctionalization to mono-, di-, and tetraepoxy derivatives is accomplished using hydrogen peroxide as a green oxidant at room temperature. Computed optimized geometries showed only slight shifts to the base planarity upon dearomatization by epoxidation, which is an important feature for DNA intercalation and bioactivity. NMR studies and comparison with theoretical values allowed the assignment of the stereochemistry of the anti- and syn-diepoxy and -tetraepoxy derivatives as well as compounds resulting from epoxide ring opening, exemplified by epoxydiol. The diepoxide is formed in an anti:syn ratio of ∼4, and the attack by nucleophiles, exemplified by ethylaniline, occurs selectively and with full conversion, using a microwave process with acetonitrile reflux for 10 min. Finally, studies of the electrostatic potential allowed the mechanisms of the formation of 4-hydroxyacridine and the regioselective reaction of diepoxyacridine with nucleophiles to be rationalized.

A study of interaction potentials for H2 adsorption in Single Walled Nano Tubes: a possible way to more realistic predictions.

A comparative analysis of interaction potentials, classified according to the parametrization method, namely Lorentz-Berthelot rules, semi-empirical or ab initio calculations, found their energy depths to scale, respectively, to ca 30K, ca 40K, and ca 60K. We draw the Potential Energy Surfaces (PESs) for a hydrogen probe molecule inside a Carbon Nano-Tube (CNT): it is shown that the adsorption energy increases with the hard radius of the interaction potential and decreases as the CNT pore enlarges. This is valid just for low-medium pressures, when hydrogen repulsions are negligible. If not, adsorption is driven by H2-H2 hard radius despite all other parameters. Monte Carlo (MC) simulations, following the Gibbs Ensemble (GE) in high density conditions, confirm that the thermodynamic equilibrium of an order-disorder phase transition show no changes throughout any of the studied potentials. We also analyse, in the Grand Canonical (GC) ensemble, the geometric and structural characteristics of square lattice bundles of Single Walled Nano Tubes (SWNTs) with regard to their influence on adsorption storage. To do so, we develop a method for independently simulate inner or outer adsorption in infinitely long nanotube lattice systems. Our results suggest a pressure range for convenient H2 storage and enlighten the influence of CNT size on adsorption performance. In addition, larger CNTs are capable to host further hydrogen layers, but only at very high pressures.

Dehydration of a polyether type extraction agent and of the corresponding K⁺ complex: insights into liquid-liquid extraction mechanisms by quantum chemical methods.

In this paper we report a quantum chemical study performed at the B3LYP/6-311G++(d,p) level of theory on structural and energetic aspects of the sequential dehydration of a tetra-hydrated polyethylene-glycol type podand (1,2-bis-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-benzene, hereafter b33) and its complex with the K⁺ cation. Thermodynamical parameters were determined by hessian quantum calculations performed using a self-consistent reaction field (SCRF) method, taking into account solvent (dichloromethane) effects. The results allowed the estimation of dehydration enthalpies, entropies and free energies for the hydrated free b33 podand and its corresponding K⁺ cation complex in dichloromethane. The low absolute values found for the dehydration free energies as well as the structural features found for the optimized structures and the corresponding basis superposition calculated interaction energies, support the hypothesis of an interfacial complexation type mechanism governing the assisted extraction of K⁺ from an aqueous toward an organic phase, in liquid/liquid extraction.

Complexation of alkali metal cations by crown-ether type podands with applications in solvent extraction: insights from quantum chemical calculations.

The complexation behavior of nine polyether type podands with a varying number of oxygen donor atoms (4-10) towards the alkali metal cations Li(+), Na(+) and K(+) was studied by quantum chemical methods at the DFT-B3LYP level of theory using the all-electron split-valence 6-311++G(d,p) basis set. The optimized structures of the complexes show a regular increase in the mean cation-oxygen distance with the coordination number. OC-CO dihedral angles of the podand arms were also found to increase with the coordination number and with the size of the cation. Maximum values for the number of strong cation-oxygen interactions (effective coordination numbers) were found for each cation (six for Li(+), seven for Na(+) and eight for K(+)). The calculated values for thermodynamic parameters relative to the binding of free and solvated cations to the podands allowed the assessment of binding constants in vacuum, in water and in dichloromethane. The estimated cation extraction constants mimic the experimental extraction trends, but their values are much larger than experimental values. Scale factors were determined to correct the values effectively. For each podand the ratios between the calculated extraction constants of Li(+) (or Na(+)) and the corresponding ones for K(+) (seen as extraction selectivities) compare acceptably with the corresponding experimental values.

Controlling product selection in the photodissociation of formaldehyde: direct quantum dynamics from the S1 barrier.

Controlling the selectivity between H(2)+CO and H+HCO in the S(1)/S(0) nonadiabatic photodissociation of formaldehyde has been investigated using direct quantum dynamics. Simulations started from the S(1) transition state have suggested that a key feature for controlling the branching ratio of ground-state products is the size of the momentum given to the wavepacket along the transition vector. Our results show that letting the wavepacket fall down from the barrier to the conical intersection with no initial momentum leads to H(2)+CO, while extra momentum toward products favors the formation of H+HCO through the same conical intersection. Quantum dynamics results are interpreted in semiclassical terms with the aid of a Mulliken-like analysis of the final population distribution among both products and the reactant on each electronic state.

Novel layer-by-layer interfacial [Ni(salen)]-polyelectrolyte hybrid films.

A novel multilayer film containing a cationic phosphonium-derivatized Ni(salen)-type complex and poly(sodium-4-styrenesulfonate (NaPSS) was assembled onto quartz, mica, and metal surfaces using the layer-by-layer (LbL) technique. Spectroscopic (UV-vis) and gravimetric (QCM) responses for the multilayer films show regular stepwise growth and the signature of strong electrostatic interactions between the component layers. The gravimetric responses indicate the presence of substantial additional (net neutral) material in the PSS layers, which XPS shows is not polyelectrolyte or salt, so charge compensation is intrinsic; we deduce the presence of space-filling solvent. Direct electrostatic interaction of the two-component layers is enhanced by a secondary noncovalent interaction between the delocalized pi-systems of the two components. Permeability of the film to the redox probe [Fe(CN)(6)](3-/4-) was studied by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Qualitatively similar results were obtained in the absence and presence of a precursor PSS/PAH multilayer, but with a general shift in kinetic and diffusional processes to longer time scales (lower frequencies) in the presence of the precursor layer and with increasing numbers of PSS/[Ni(salen)] bilayers. Quantitatively, the EIS data were interpreted using a capillary membrane model (CMM) to yield values of coverage, apparent charge transfer resistance, double-layer capacitance, pore size, and diffusion coefficient. The coverage values were consistent with a model in which there are no preferential growth sites and the surface charge density is independent of the number of bilayers.

The molecular dissociation of formaldehyde at medium photoexcitation energies: A quantum chemistry and direct quantum dynamics study.

The mechanisms of radiationless decay involved in the photodissociation of formaldehyde into H(2) and CO have been investigated using complete active space self-consistent field (CASSCF) calculations and direct dynamics variational multiconfiguration Gaussian (DD-vMCG) quantum dynamics in the S(1), T(1), and S(0) states. A commonly accepted scheme involves Fermi Golden Rule internal conversion from S(1) followed by dissociation of vibrationally hot H(2)CO in S(0). We recently proposed a novel mechanism [M. Araujo et al., J. Phys. Chem. A 112, 7489 (2008)] whereby internal conversion and dissociation take place in concert through a seam of conical intersection between S(1) and S(0) after the system has passed through an S(1) transition barrier. The relevance of this mechanism depends on the efficiency of tunneling in S(1). At lower energy, an alternative scheme to internal conversion involves intersystem crossing via T(1) to regenerate the reactant before the S(0) barrier to dissociation. We propose here a previously unidentified mechanism leading directly to H(2) and CO products via T(1). This channel opens at medium energies, near or above the T(1) barrier to dissociation and still lower than the S(1) barrier, thus making T(1) a possible shortcut to molecular dissociation.

Prot-2S: a new python web tool for protein secondary structure studies.

Prot-2S is a bioinformatics web application devised to analyse the protein chain secondary structures (2S) (http:/ /www.requimte.pt:8080/Prot-2S/). The tool is built on the RCSB Protein Data Bank PDB and DSSP application/files and includes calculation/graphical display of amino acid propensities in 2S motifs based on any user amino acid classification/code (for any particular protein chain list). The interface can calculate the 2S composition, display the 2S subsequences and search for DSSP non-standard residues and for pairs/triplets/quadruplets (amino acid patterns in 2S motifs). This work presents some Prot-2S applications showing its usefulness in protein research and as an e-learning tool as well.

Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices.

The cancer diagnostic is a complex process and, sometimes, the specific markers can interfere or produce negative results. Thus, new simple and fast theoretical models are required. One option is the complex network graphs theory that permits us to describe any real system, from the small molecules to the complex genetic, neural or social networks by transforming real properties in topological indices. This work converts the protein primary structure data in specific Randic's star networks topological indices using the new sequence to star networks (S2SNet) application. A set of 1054 proteins were selected from previous works and contains proteins related or not with two types of cancer, human breast cancer (HBC) and human colon cancer (HCC). The general discriminant analysis method generates an input-coded multi-target classification model with the training/predicting set accuracies of 90.0% for the forward stepwise model type. In addition, a protein subset was modified by single amino acid mutations with higher log-odds PAM250 values and tested with the new classification if can be related with HBC or HCC. In conclusion, we shown that, using simple input data such is the primary protein sequence and the simples linear analysis, it is possible to obtain accurate classification models that can predict if a new protein related with two types of cancer. These results promote the use of the S2SNet in clinical proteomics.

Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices.

The huge amount of new proteins that need a fast enzymatic activity characterization creates demands of protein QSAR theoretical models. The protein parameters that can be used for an enzyme/non-enzyme classification includes the simpler indices such as composition, sequence and connectivity, also called topological indices (TIs) and the computationally expensive 3D descriptors. A comparison of the 3D versus lower dimension indices has not been reported with respect to the power of discrimination of proteins according to enzyme action. A set of 966 proteins (enzymes and non-enzymes) whose structural characteristics are provided by PDB/DSSP files was analyzed with Python/Biopython scripts, STATISTICA and Weka. The list of indices includes, but it is not restricted to pure composition indices (residue fractions), DSSP secondary structure protein composition and 3D indices (surface and access). We also used mixed indices such as composition-sequence indices (Chou's pseudo-amino acid compositions or coupling numbers), 3D-composition (surface fractions) and DSSP secondary structure amino acid composition/propensities (obtained with our Prot-2S Web tool). In addition, we extend and test for the first time several classic TIs for the Randic's protein sequence Star graphs using our Sequence to Star Graph (S2SG) Python application. All the indices were processed with general discriminant analysis models (GDA), neural networks (NN) and machine learning (ML) methods and the results are presented versus complexity, average of Shannon's information entropy (Sh) and data/method type. This study compares for the first time all these classes of indices to assess the ratios between model accuracy and indices/model complexity in enzyme/non-enzyme discrimination. The use of different methods and complexity of data shows that one cannot establish a direct relation between the complexity and the accuracy of the model.

Copper acetylacetonate anchored onto amine-functionalised clays.

Copper (II) acetylacetonate was immobilised directly onto two clays, laponite (Lap) and K10-montmorillonite (K10), and after their amine functionalisation with (3-aminopropyl)triethoxysilane (APTES). All the materials were characterised by nitrogen adsorption isotherms at -196 degrees C, elemental analysis, TG-DSC, XRD, and IR spectroscopy. The K10-based materials were also characterised by XPS. The APTES-functionalised K10 showed higher copper loading than K10, indicating that the clay functionalisation enhanced the complex immobilisation; on the contrary, in Lap-based materials higher metal content was obtained by direct complex anchoring, probably due to the delaminated nature of Lap which induced the particles aggregation on functionalisation with APTES. All the results pointed out that the Cu complex was anchored onto the amine-functionalised clays by Schiff condensation between the amine groups of anchored APTES and the carbonyl groups of the acetylacetonate ligand, whereas direct immobilisation proceeded mostly through interaction between the metal centre and the clay surface hydroxyl groups.