Various models of the complex formation between polyelectrolyte chains and oppositely charged macroions are reviewed. In recent years, a great deal of knowledge of the multitude of possible polyelectrolyte conformations at the macroion surface has been accumulated, which consequently has led to increasing interest in using such complexes in the design of nanomaterials. This review focuses on key studies relating to the effects of various physico-chemical parameters on complex formation and areas for future research are identified.

Thousands of biochemical reactions with characterized activities are “orphan,” meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, limiting protein engineering applications. Associating orphan and novel reactions with known biochemistry and suggesting enzymes to catalyze them is a daunting problem. We propose the method BridgIT to identify candidate genes and catalyzing proteins for these reactions. This method introduces information about the enzyme binding pocket into reaction-similarity comparisons. BridgIT assesses the similarity of two reactions, one orphan and one well-characterized nonorphan reaction, using their substrate reactive sites, their surrounding structures, and the structures of the generated products to suggest enzymes that catalyze the most-similar nonorphan reactions as candidates for also catalyzing the orphan ones. We performed two large-scale validation studies to test BridgIT predictions against experimental biochemical evidence. For the 234 orphan reactions from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 2011 (a comprehensive enzymatic-reaction database) that became nonorphan in KEGG 2018, BridgIT predicted the exact or a highly related enzyme for 211 of them. Moreover, for 334 of 379 novel reactions in 2014 that were later cataloged in KEGG 2018, BridgIT predicted the exact or highly similar enzymes. BridgIT requires knowledge about only four connecting bonds around the atoms of the reactive sites to correctly annotate proteins for 93% of analyzed enzymatic reactions. Increasing to seven connecting bonds allowed for the accurate identification of a sequence for nearly all known enzymatic reactions.

Heteroaggregation of engineered nanoparticles with suspended particulate matter in theory and practice: a roadmap for understanding and determining attachment efficiencies.

The electrostatic driven complex formation between a weak polyampholyte chain and one positively charged nanoparticle is investigated using Monte Carlo simulations. The influence of parameters such as the polyampholyte contour length, number and size of blocks, nanoparticle surface charge density, and solution properties, such as the pH and ionic concentration, on the PA titration curves is investigated. It is shown that the presence of one positively charged nanoparticle significantly modifies the acid/base properties of the weak polyampholyte by, on the one hand, promoting the formation of negatively charged monomers and, on the other hand, limiting the number of positively charged monomers. The electrostatic interactions of this system can be modified by pH, ionic concentration, and nanoparticle surface charge. The competition between attractive and repulsive, intramolecular and intermolecular electrostatic interactions leads to a wide range of possible PA conformations at the nanoparticle surface, which have a direct impact on the nanoparticle stabilized or destabilized solutions. Extended conformations, electrostatic rosettes, and dense multiplayer structures are observed. Nonetheless, the intramolecular interactions between the positively and negatively charged PA monomers, in particular at the isoelectric point, are found to play important and subtle roles for both the isolated and adsorbed chain conformations. It is also found that nanoparticle charge inversion is an important ingredient for the formation of multilayer structures at the nanoparticle surface.

Monte Carlo simulations have been used to study two different models for a weak linear polyelectrolyte in the presence of nanoparticles: (i) a rodlike and (ii) a flexible polyelectrolytes. The use of simulated annealing has made it possible to simulate a polyelectrolyte chain in the presence of several nanoparticles by improving conformation sampling and avoiding multiple minima problems when dense conformations are produced. Nanoparticle distributions along the polymer backbone were analyzed versus the ionic concentration, polyelectrolyte stiffness, and nanoparticle surface charge. Titration curves were calculated and the influences of the ionic concentration, solution pH, and number of adsorbed nanoparticles on the acid/base polyelectrolyte properties have been systematically investigated. The subtle balance of attractive and repulsive interactions has been discussed, and some characteristic conformations are presented. The comparison of the two limit models provides a good representation of the stiffness influence on the complex formation. In some conditions, overcharging was obtained and presented with respect to both the polyelectrolyte and nanoparticle as the central element. Finally, the charge mobility influence along the polyelectrolyte backbone was investigated by considering annealed and quenched polyelectrolyte chains.

First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.

The conformation and titration curves of weak polyampholytes are examined using Monte Carlo simulations with screened Coulomb potentials in the Grand Canonical ensemble. Two different types of monomers are considered. Depending on the solution pH, monomers A are weak acidic sites that can either be negatively charged or uncharged (as carboxylic groups), whereas monomers B are weak basic sites that can either be positively charged or uncharged (as amino groups). The influence of the chain stiffness, primary structure, and ionic concentration on the acid/base properties of the polyampholyte chains are systematically investigated. By adjusting the pH values, titration curves and then the fractions of positively and negatively ionized charged monomers are calculated. Stiffness influence is estimated by comparing two models of chain: a fully flexible and a rod-like polyampholyte. Different primary structures such as statistical (diblock, octablock, and alternating) and random polyampholytes are also considered. We demonstrate that the primary structure plays important roles in the acid/base properties as well as the charge distribution along the polymer backbone of a statistical rod-like polyampholyte. When flexible polyampholytes are considered, polyampholyte conformations promote the attractive electrostatic interactions between positively and negatively charged monomers, hence leading to more or less compact conformations and acid/base properties relatively different in comparison to the rod-like polyampholytes. Various conformations such as extended, globular, and pearl-necklace conformations are found in good agreement with the literature by adjusting the interaction parameter between monomers and monomer stoichiometry.

Insight into the conformations and aggregation of alginic acid was gained by measuring its diffusion coefficient at very dilute concentrations using fluorescence correlation spectroscopy. Both the pH and ionic strength (I) had an important influence on the diffusion coefficient of the polysaccharide. For pH, three effects were isolated: (i) below pH 4, the charge density decreased causing increased aggregation; (ii) between pH 4 and 8, a molecular expansion was observed with increasing pH, whereas (iii) above pH 8 some dissociation of the polymer was observed. Increasing I from 0.001 to 0.1 M resulted in a ca. 20% increase in the diffusion coefficient. By coupling these measurements to molar mass determinations obtained by size exclusion chromatography and monomer size estimations determined from ab initio calculations, it was possible to determine the radii of gyration via de Gennes renormalization theory. From diffusion coefficients and radii of gyration obtained as a function of ionic strength, persistence lengths (total, electrostatic, and intrinsic) were calculated from the Benoit-Doty relationship.