How Does Ammonium Dynamically Interact with Benzene in Aqueous Media? A First Principle Study Using the Car−Parrinello Molecular Dynamics Method

Complexes of Alkaline and Ammonium Cations with Dopamine and Eumelanin Precursors: Dissecting the Role of Noncovalent Cation-π and Cation-Lone Pair (σ-Type) Interactions

Cation-π interactions and their possible competition with other noncovalent interactions (NCI) might play a key role in both dopamine- and eumelanin-based bioinspired materials. In this contribution, to unravel the delicate interplay between cation-π interactions and other possible competing forces, the configurational space of noncovalent complexes formed by dopamine or eumelanin precursors (o-benzoquinone, DHI and a semiquinone dimer) and three different cations (Na⁺, K⁺, and NH₄⁺) is sampled by means of accurate ab initio calculations. To this end, we resort to the mp2^mod method, recently validated by us for benzene-, phenol-, and catechol-cation complexes, whose computational convenience allows for an extensive exploration of the cation-molecule interaction energy surface, by sampling a total of more than 10⁴ arrangements. The mp2^mod interaction energy landscapes reveal that, besides the expected cation-π driven arrangements, for all considered molecule-cation pairs the most stable complexes are found when the cation lies within the plane containing the six-membered ring, thus maximizing the σ-type interaction with the oxygen's lone pairs. Due to the loss of aromaticity, the σ-type/cation-π strength ratio is remarkably large in o-benzoquinone, where cation-π complexes seem unlikely to be formed. The above features are shared among all considered cations but are significantly larger when considering the smaller Na⁺. Besides delivering a deeper insight onto the NCI network established by the considered precursors in the presence of ions, the present results can serve as a reference database to validate or refine lower level methods, as, for instance, the force fields employed in classical simulations.

Explicit Representation of Cation-π Interactions in Force Fields with 1/r4 Nonbonded Terms

The binding energies for cation-π complexation are underestimated by traditional fixed-charge force fields owing to their lack of explicit treatment of ion-induced dipole interactions. To address this deficiency, an explicit treatment of cation-π interactions has been introduced into the OPLS-AA force field. Following prior work with atomic cations, it is found that cation-π interactions can be handled efficiently by augmenting the usual 12-6 Lennard-Jones potentials with 1/r⁴ terms. Results are provided for prototypical complexes as well as protein-ligand systems of relevance for drug design. Alkali cation, ammonium, guanidinium, and tetramethylammonium were chosen for the representative cations, while benzene and six heteroaromatic molecules were used as the π systems. The required nonbonded parameters were fit to reproduce structure and interaction energies for gas-phase complexes from density functional theory (DFT) calculations at the ωB97X-D/6-311++G(d,p) level. The impact of the solvent was then examined by computing potentials of mean force (pmfs) in both aqueous and tetrahydrofuran (THF) solutions using the free-energy perturbation (FEP) theory. Further testing was carried out for two cases of strong and one case of weak cation-π interactions between druglike molecules and their protein hosts, namely, the JH2 domain of JAK2 kinase and macrophage migration inhibitory factor. FEP results reveal greater binding by 1.5-4.4 kcal/mol from the addition of the explicit cation-π contributions. Thus, in the absence of such treatment of cation-π interactions, errors for computed binding or inhibition constants of 10¹-10³ are expected.

Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution

Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH₃⁺ and RN(CH₃)₃⁺) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA⁺) and tetraethylammonium (TEA⁺). Polarizable molecular models are calibrated for NH₄⁺, TMA⁺, and TEA⁺ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH₄⁺ > TMA⁺ > TEA⁺, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA⁺ (the largest ion), the most stable solvent-separated complexes involve TMA⁺ (the intermediate-size ion).

Aggregation, Adsorption, and Morphological Transformation of Graphene Oxide in Aqueous Solutions Containing Different Metal Cations

The colloidal behavior of graphene oxide (GO) has been extensively studied in the presence of common environmental cations, but the aggregation, adsorption, and morphological transformation of GO under heavy metal ions have not been investigated. We observed that heavy metal cations (Cr³⁺, Pb²⁺, Cu²⁺, Cd²⁺, Ag⁺) destabilized GO suspension more aggressively than common cations (Ca²⁺, Mg²⁺, Na⁺, K⁺). In addition to electric double-layer (EDL) suppression, heavy metal cations can easily cross the EDL, bind to GO surface, and then change the surface potential, which is a more efficient pathway for GO aggregation. According to aggregation kinetics, the destabilizing ability of cations follows the order of Cr³⁺ ≫ Pb²⁺ > Cu²⁺ > Cd²⁺ > Ca²⁺ > Mg²⁺ ≫ Ag⁺ > K⁺ > Na⁺. The destabilizing capability of metal cations is consistent with their adsorption affinity with GO, which is determined by their electronegativity and hydration shell thickness. GO nanosheets can be transformed to 1D tube-like carbon material, 2D multiple overlapped GO plane, and 3D sphere-like particles during aggregation, thereby combined to form a sphere-like aggregated GO, which is for the first time observed by TEM and AFM images. Therefore, the aggregation of GO 2D nanosheets follows the Schulze-Hardy rule, which is usually used for spherical particles. An integrative process of adsorption-transformation-aggregation is proposed to better understand the nanomaterial (e.g., GO) colloidal behavior, environmental risk, self-assembly process, and application as a novel adsorbent.

Estimating the binding ability of onium ions with CO2 and π systems: a computational investigation

The impact of increasing methyl substitution on onium ions in their complexes with CO₂ and aromatic systems has been analyzed using DFT calculations.

Discovery of novel allosteric effectors based on the predicted allosteric sites for Escherichia coli D-3-phosphoglycerate dehydrogenase

D-3-phosphoglycerate dehydrogenase (PGDH) from Escherichia coli catalyzes the first critical step in serine biosynthesis, and can be allosterically inhibited by serine. In a previous study, we developed a computational method for allosteric site prediction using a coarse-grained two-state Gō Model and perturbation. Two potential allosteric sites were predicted for E. coli PGDH, one close to the active site and the nucleotide binding site (Site I) and the other near the regulatory domain (Site II). In the present study, we discovered allosteric inhibitors and activators based on site I, using a high-throughput virtual screen, and followed by using surface plasmon resonance (SPR) to eliminate false positives. Compounds 1 and 2 demonstrated a low-concentration activation and high-concentration inhibition phenomenon, with IC₅₀ values of 34.8 and 58.0 µM in enzymatic bioassays, respectively, comparable to that of the endogenous allosteric effector, L-serine. For its activation activity, compound 2 exhibited an AC₅₀ value of 34.7 nM. The novel allosteric site discovered in PGDH was L-serine- and substrate-independent. Enzyme kinetics studies showed that these compounds influenced K_m, k_cat, and k_cat/K_m. We have also performed structure-activity relationship studies to discover high potency allosteric effectors. Compound 2-2, an analog of compound 2, showed the best in vitro activity with an IC₅₀ of 22.3 µM. Compounds targeting this site can be used as new chemical probes to study metabolic regulation in E. coli. Our study not only identified a novel allosteric site and effectors for PGDH, but also provided a general strategy for designing new regulators for metabolic enzymes.

Ion size influence on the Ar solvation shells of M(+)-C6F6 clusters (M = Na, K, Rb, Cs)

The size-specific influence of alkali metal ions in the gradual transition from cluster rearrangement to solvation dynamics is investigated by means of molecular dynamics simulations for alkali metal cation-hexafluorobenzene systems, M(+)-C(6)F(6) (M = Na, K, Rb and Cs), surrounded by Ar atoms. To analyze such transition, different small aggregates of the M(+)-C(6)F(6)-Ar(n) (n = 1, ..., 30) type and M(+)-C(6)F(6) clusters solvated by about 500 Ar atoms are considered. The Ar-C(6)F(6) interaction contribution has been described using two different formalisms, based on the interaction decomposition in atom-bond and in atom-effective atom terms, which have been applied to study the small aggregates and to investigate the Ar solvated M(+)-C(6)F(6) clusters, respectively. The selectivity of the promoted phenomena from the M(+) ion size and their dependence from the number of Ar atoms is characterized.

Real-world predictions from ab initio molecular dynamics simulations

In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.

Size-Specific Interaction of Alkali Metal Ions in the Solvation of M+−Benzene Clusters by Ar Atoms

The size-specific influence of the M+ alkali ion (M = Li, Na, K, Rb, and Cs) in the solvation process of the M+-benzene clusters by Ar atoms is investigated by means of molecular dynamic simulations. To fully understand the behavior observed in M+-bz-Ar(n) clusters, solvation is also studied in clusters containing either M+ or benzene only. The potential energy surfaces employed are based on a semiempirical bond-atom decomposition, which has been developed previously by some of the authors. The outcome of the dynamics is analyzed by employing radial distribution functions, studying the evolution of the distances between the Ar atoms and the alkali ion M+ or the benzene molecule for all M+-bz-Ar(n) clusters. For all members, in the M+-bz series, the benzene molecule (bz) is found to remain strongly bound to M+ even in the presence of solvent atoms. The radial distribution functions for the heavier clusters (K+-bz, Rb+-bz, and Cs+-bz), are found to be different than for the lighter (Na+-bz and Li+-bz) ones.