A Martini Coarse Grained Model of Citrate-Capped Gold Nanoparticles Interacting with Lipid Bilayers

Citrate capping is one of the most common strategies to achieve the colloidal stability of Au nanoparticles (NPs) with diameters ranging from a few to hundreds of nanometers. Citrate-capped Au nanoparticles (CNPs) represent a step of the synthesis of Au NPs with specific functionalities, as CNPs can be further functionalized via ligand-exchange reactions, leading to the replacement of citrate with other organic ligands. In vitro, CNPs are also used to address the fundamental aspects of NP-membrane interactions, as they can directly interact with cells or model cell membranes. Their affinity for the bilayer is again mediated by the exchange of citrate with lipid molecules. Here, we propose a new computational model of CNPs compatible with the coarse grained Martini force field. The model, which we develop and validate through an extensive comparison with new all-atom molecular dynamics (MD) simulations and UV-vis and Fourier transform infrared spectroscopy data, is aimed at the MD simulation of the interaction between citrate-capped NPs and model phosphatidylcholine lipid membranes. As a test application we show that, during the interaction between a single CNP and a flat planar 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer, the citrate coating is spontaneously replaced by lipids on the surface of Au NPs, while the NP size and shape determine the final structural configuration of the NP-bilayer complex.

Simulation Insight into the Synergic Role of Citrate and Polyaspartic Peptide in Biomineralization

Hydroxyapatite (HAP) is one of the most important inorganic components in biological minerals such as bones and teeth. More than 90% of the total citrate is accumulated in human bones and other biomineralized tissues. In addition, mineralizing proteins are enriched in glutamate and aspartate residues, which are important for their mineral-regulating properties. However, how citrate ions (CITs) and/or acidic amino acids regulate the formation of HAP is still unclear. In this work, molecular dynamics simulations were performed to study how CIT regulates the adsorption behavior of polyaspartic acid (PASP) on the HAP surface in the calcium phosphate solution. The simulation results indicate that PASP can be used as an ion chelator to complex Ca²⁺ and can serve as templates for HAP mineralization by templating the distribution of Ca²⁺ on its surface, which are attributed to the -COO^- and α-helix structure. Most importantly, the orientation distributions of PASP in all systems are narrower with the help of CIT, thereby PASP can be adsorbed on the HAP surface stably with a "lying-down" orientation. This indicates that CIT can be used as a bridging agent to bond the acidic peptide to the HAP surface in biomineralization. Thus, the synergic role of CIT and the acidic peptide on the HAP surface were revealed in this work, which can provide new insights into the interfacial phenomena during the biomineralization.

Equilibria and Dynamics of Sodium Citrate Aqueous Solutions: The Hydration of Citrate and Formation of the Na3Cit0 Ion Aggregate

Sodium citrate (Na₃Cit) has a crucial role in many biological and industrial processes. Yet, quantitative information on its hydration and the ion association between Na⁺ and Cit^3- ions in a broad range of salt concentrations is still lacking. In this work, we study both ion association equilibria and relaxation dynamics of sodium citrate solutions by combining potentiometry, spectrophotometry, and dielectric spectroscopy. From photometric and potentiometric measurements, we detect the formation of the NaCit^2- ion-pair and the neutral Na₃Cit⁰ ion aggregate in a wide range of ionic strengths (0.5-4 M). Due to its remarkable stability, the latter becomes the prevailing species at higher salt concentrations. In the dielectric spectra, we observe the dipolar relaxation of Cit^3- and NaCit^2- and two solvent-related processes, associated with the collective rearrangement of the H-bond network (cooperative water mode) and the H-bond flip of water molecules (fast water mode). Unlike numerous other salt solutions, the relaxation time of the cooperative mode scales with the viscosity indicating that the strongly hydrated anion fits well into the water network. That is, the stabilizing effect of anion-solvent interactions on the H-bond network outweighs the destructive impact of the cations as the latter are only present at low concentration, due to strong ion association. In conclusion, the affinity of citrate toward Na⁺ binding not only governs solution equilibria but also has a strong impact on water dynamics.

Connecting energetics to dynamics in particle growth by oriented attachment using real-time observations

The interplay between crystal and solvent structure, interparticle forces and ensemble particle response dynamics governs the process of crystallization by oriented attachment (OA), yet a quantitative understanding is lacking. Using ZnO as a model system, we combine in situ TEM observations of single particle and ensemble assembly dynamics with simulations of interparticle forces and responses to relate experimentally derived interparticle potentials to the underlying interactions. We show that OA is driven by forces and torques due to a combination of electrostatic ion-solvent correlations and dipolar interactions that act at separations well beyond 5 nm. Importantly, coalignment is achieved before particles reach separations at which strong attractions drive the final jump to contact. The observed barrier to attachment is negligible, while dissipative factors in the quasi-2D confinement of the TEM fluid cell lead to abnormal diffusivities with timescales for rotation much less than for translation, thus enabling OA to dominate.

Retracted: Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies

Retraction: Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies by Jehoon Kim, Mark R. H. Krebs and Bernhardt L. Trout The above article from the Journal of Pharmacy and Pharmacology, first published online on 4 August 2017 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal Editor-in-Chief, Professor David Jones, and John Wiley & Sons Ltd. The authors discovered that the analysis of simulations was faulty making the data incorrect. Reference Kim J et al. Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies. J Pharm Pharmacol 2017. https://doi.org/10.1111/jphp.12787.

Ionization and Conformational Equilibria of Citric Acid: Delocalized Proton Binding in Solution

The microspeciation of citric acid is studied by analyzing NMR titration data. When the site binding (SB) model, which assumes fully localized proton binding to the carboxylic groups, is used to obtain microscopic energy parameters (dissociation constants, pair and triplet interaction energies between charged carboxylate groups), contradictory results are obtained. The resulting macroscopic constants are in very good agreement with the values reported in the literature using potentiometry. However, the found pair interaction energy between the terminal carboxylates and the triplet interaction energy are physically meaningless. To solve this apparent contradiction, we consider the possibility of delocalized proton binding, so that the proton can be exchanged at high velocity in the NMR time scale through short, strong, low-barrier (SSLB) hydrogen bonds. With this aim, ab initio MP2 calculations using the SMD polarizable continuum model for the solvent were performed and the fully roto-microspeciation elucidated. First, fully localized proton binding was assumed, and the resulting microstate probabilities are in reasonable agreement with those reported in previous works that use selective blocking of the carboxylic groups. They are, however, in clear disagreement with the microstate probabilities derived from the NMR titration data, which predict, within a very narrow confidence interval, a unique microspecies for the symmetric di-ionized form. Moreover, counterintuitively, the interaction between terminal charged groups is much larger than that between central and terminal groups. As a consequence, we have explored the possibility of delocalized proton binding by calculating the energy of intermediate proton positions between two carbolxylic groups. The results reveal that the exchange of the proton through the hydrogen bonds is in some cases produced without energetic barrier. This effect is specially relevant in the di-ionized form, with all the most stable conformations forming a SSLB, which together would constitute the only microstate detected by NMR. An alternative reaction scheme for the ionization process, based on proton delocalization, is proposed.

Understanding and Designing the Gold-Bio Interface: Insights from Simulations

Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.

Probing the influence of citrate-capped gold nanoparticles on an amyloidogenic protein

Nanoparticles (NPs) are known to exhibit distinct physical and chemical properties compared with the same materials in bulk form. NPs have been repeatedly reported to interact with proteins, and this interaction can be exploited to affect processes undergone by proteins, such as fibrillogenesis. Fibrillation is common to many proteins, and in living organisms, it causes tissue-specific or systemic amyloid diseases. The nature of NPs and their surface chemistry is crucial in assessing their affinity for proteins and their effects on them. Here we present the first detailed structural characterization and molecular mechanics model of the interaction between a fibrillogenic protein, β2-microglobulin, and a NP, 5 nm hydrophilic citrate-capped gold nanoparticles. NMR measurements and simulations at multiple levels (enhanced sampling molecular dynamics, Brownian dynamics, and Poisson-Boltzmann electrostatics) explain the origin of the observed protein perturbations mostly localized at the amino-terminal region. Experiments show that the protein-NP interaction is weak in the physiological-like, conditions and do not induce protein fibrillation. Simulations reproduce these findings and reveal instead the role of the citrate in destabilizing the lower pH protonated form of β2-microglobulin. The results offer possible strategies for controlling the desired effect of NPs on the conformational changes of the proteins, which have significant roles in the fibrillation process.

Developing accurate molecular mechanics force fields for conjugated molecular systems

A rapid method to parameterize the intramolecular component of classical force fields is proposed and applied to a molecular semiconductor, oligomers of conjugated polymers and a biological chromophore.

Structure and properties of citrate overlayers adsorbed at the aqueous Au(111) interface

One of the most common means of gold nanoparticle (AuNP) biofunctionalization involves the manipulation of precursor citrate-capped AuNPs via ligand displacement. However, the molecular-level structural characteristics of the citrate overlayer adsorbed at the aqueous Au interface at neutral pH remain largely unknown. Access to atomistic-scale details of these interfaces will contribute much needed insight into how AuNPs can be manipulated and exploited in aqueous solution. Here, the structures of such citrate overlayers adsorbed at the aqueous Au(111) interface at pH 7 are predicted and characterized using atomistic molecular dynamics simulations, for a range of citrate surface densities. We find that the overlayers are disordered in the surface density range considered, and that many of their key characteristics are invariant with surface density. In particular, we predict the overlayers to have 3-D, rather than 2-D, morphologies, with the anions closest to the gold surface being oriented with their carboxylate groups pointing away from the surface. We predict both striped and island morphologies for our overlayers, depending on the citrate surface density, and in all cases we find bare patches of the gold surface are present. Our simulations suggest that both citrate-gold adsorption and citrate-counterion pairing contribute to the stability of these citrate overlayer morphologies. We also calculate the free energy of adsorption at the aqueous Au(111) interface of a single citrate molecule, and compare this with the corresponding value for a single arginine molecule. These findings enable us to predict the conditions under which ligand displacement of surface-adsorbed citrate by arginine may take place. Our findings represent the first steps toward elucidating a more elaborate, detailed atomistic-scale model relating to the biofunctionalization of citrate-capped AuNPs.