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

Structure and function of an intermediate GPCR-Gαβγ complex

Unraveling the signaling roles of intermediate complexes is pivotal for G protein-coupled receptor (GPCR) drug development. Despite hundreds of GPCR-Gαβγ structures, these snapshots primarily capture the fully activated end-state complex. Consequently, a comprehensive understanding of the conformational transitions during GPCR activation and the roles of intermediate GPCR-G protein complexes in signaling remain elusive. Guided by a conformational landscape profiled by 19 F quantitative NMR ( 19 F-qNMR) and Molecular Dynamics (MD) simulations, we resolved the structure of an unliganded GPCR-G protein intermediate complex by blocking its transition to the fully activated end-state complex. More importantly, we presented direct evidence that the intermediate GPCR-Gαsβγ complex initiates a rate-limited nucleotide exchange without progressing to the fully activated end-state complex, thereby bridging a significant gap in our understanding the complexity of GPCR signaling. Understanding the roles of individual conformational states and their complexes in signaling efficacy and bias will help us to design drugs that discriminately target a disease-related conformation.

Iron oxide magnetic aggregates: Aspects of synthesis, computational approaches and applications

Superparamagnetic magnetite nanoparticles have been central to numerous investigations in the past few decades for their use in many applications, such as drug delivery, medical diagnostics, magnetic separation, and material science. However, the properties of single magnetic nanoparticles are sometimes not sufficient to accomplish tasks where a strong magnetic response is required. In light of this, aggregated magnetite nanoparticles have been proposed as an alternative advanced material, which may expand and combine some of the advantages of single magnetic nanoparticles, including superparamagnetism, with an enhanced magnetic moment and increased colloidal stability. This review comprehensively discusses the current literature on aggregates made of magnetic iron oxide nanoparticles. This review is divided into three sections. First, the current synthetic strategies for magnetite nanoparticle aggregates are discussed, together with the influence of different stabilizers on the primary crystals and the final aggregate size and morphology. The second section is dedicated to computational approaches, such as density functional methods (which permit accurate predictions of electronic and magnetic properties and shed light on the behavior of surfactant molecules on iron oxide surfaces) and molecular dynamics simulations (which provide additional insight into the influence of ligands on the surface chemistry of iron oxide nanocrystals). The last section discusses current and possible future applications of iron oxide magnetic aggregates, including wastewater treatment, water purification, medical applications, and magnetic aggregates for materials displaying structural colors.

Structural Diversity of Protonated Citric Acid-Ammonia Clusters and Its Atmospheric Implication

Various acid-base molecular clusters involving organic species can serve as precursors that play important roles in the formation of an atmospheric aerosol. Due to its structural flexibility and its ability to form multiple hydrogen bonds, citric acid acts as a key species in forming clusters that are critical in the nucleation of related aerosol precursors. Thus, it is provoking to characterize the structures of these clusters at the molecular level. In this paper, protonated citric acid-ammonia clusters of various sizes were generated by electrospray ionization and studied by tandem mass spectrometry. The structures of [(CA)2+NH4]1+ and [(CA)4+NH4]1+ were further characterized by the method of infrared photodissociation (IRPD) spectroscopy. Combined with theoretical calculations, it is found that the most stable structures of the dimeric and tetrameric isomers show the shapes of an ingot and a lantern, respectively. It has been revealed that the temperature has a great effect on the contributions of different isomers for both dimers and tetramers. The dominat isomers are found to have more open structures at higher temperatures, facilitating the growth of clusters through new hydrogen bonds.

Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes

This article reviews the state of the art of the studies on charge regulation (CR) effects in flexible weak polyelectrolytes (FWPE). The characteristic of FWPE is the strong coupling of ionization and conformational degrees of freedom. After introducing the necessary fundamental concepts, some unconventional aspects of the the physical chemistry of FWPE are discussed. These aspects are: (i) the extension of statistical mechanics techniques to include ionization equilibria and, in particular, the use of the recently proposed Site Binding-Rotational Isomeric State (SBRIS) model, which allows the calculation of ionization and conformational properties on the same foot; (ii) the recent progresses in the inclusion of proton equilibria in computer simulations; (iii) the possibility of mechanically induced CR in the stretching of FWPE; (iv) the non-trivial adsorption of FWPE on ionized surfaces with the same charge sign as the PE (the so-called "wrong side" of the isoelectric point); (v) the influence of macromolecular crowding on CR.

Fully Symmetric Cyclodextrin Polycarboxylates: How to Determine Reliable Protonation Constants from NMR Titration Data

Acid-base properties of cyclodextrins (CDs), persubstituted at C-6 by 3-mercaptopropionic acid, sualphadex (Suα-CD), subetadex (Suβ-CD) and sugammadex (Suγ-CD, the antidote of neuromuscular blocking steroids) were studied by ¹H NMR-pH titrations. For each CD, the severe overlap in protonation steps prevented the calculation of macroscopic pK_a values using the standard data fitting model. Considering the full symmetry of polycarboxylate structures, we reduced the number of unknown NMR parameters in the "Q-fitting" or the novel "equidistant macroscopic" evaluation approaches. These models already provided pK_a values, but some of them proved to be physically unrealistic, deceptively suggesting cooperativity in carboxylate protonations. The latter problem could be circumvented by adapting the microscopic site-binding (cluster expansion) model by Borkovec, which applies pairwise interactivity parameters to quantify the mutual basicity-decreasing effect of carboxylate protonations. Surprisingly, only a single averaged interactivity parameter could be calculated reliably besides the carboxylate 'core' microconstant for each CD derivative. The speciation of protonation isomers hence could not be resolved, but the optimized microscopic basicity parameters could be converted to the following sets of macroscopic pK_a values: 3.84, 4.35, 4.81, 5.31, 5.78, 6.28 for Suα-CD; 3.82, 4.31, 4.73, 5.18, 5.64, 6.06, 6.54 for Suβ-CD and 3.83, 4.28, 4.65, 5.03, 5.43, 5.81, 6.18, 6.64 for Suγ-CD. The pH-dependent charge of these compounds can now be accurately calculated, in support of designing new analytical methods to exploit their charge-dependent molecular recognition such as in cyclodextrin-aided chiral capillary electrophoresis.

Role of pKA in Charge Regulation and Conformation of Various Peptide Sequences

Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged groups. The latter is determined by the amino acid sequence in the peptide chain. In our previous work we introduced a simple coarse-grained model of a flexible peptide. We validated it against experiments, demonstrating its ability to quantitatively predict charge on various peptides in a broad range of pH. In the current work, we investigated two types of peptide sequences: diblock and alternating, each of them consisting of an equal number of amino acids with acid and base side-chains. We showed that changing the sequence while keeping the same overall composition has a profound effect on the conformation, whereas it practically does not affect total charge on the peptide. Nevertheless, the sequence significantly affects the charge state of individual groups, showing that the zero net effect on the total charge is a consequence of unexpected cancellation of effects. Furthermore, we investigated how the difference between the pKA of acid and base side chains affects the charge and conformation of the peptide, showing that it is possible to tune the charge-regulating properties by following simple guiding principles based on the pKA and on the amino acid sequence. Our current results provide a theoretical basis for understanding of the complex coupling between the ionisation and conformation in flexible polyampholytes, including synthetic polymers, biomimetic materials and biological molecules, such as intrinsically disordered proteins, whose function can be regulated by changes in the pH.

Arsenite oxidation and arsenic adsorption on birnessite in the absence and the presence of citrate or EDTA

Birnessite not only oxidizes arsenite into arsenate but also interacts with organic matter in various ways. However, effects of organic matter on interaction between As and birnessite remain unclear. This study investigated effects of citrate and EDTA (3.12 and 2.05 mM, respectively) on oxidation of As(III) (1.07 mM) and adsorption of As(V) (0.67 mM) on birnessite (5.19 mM as Mn) at near-neutral pH. We found that As(V) adsorption on birnessite was enhanced by citrate and EDTA, which resulted from the increase in active adsorption sites via dissolution of birnessite. In comparison with citrate batches, more As was adsorbed on birnessite in EDTA batches, where dissolved Mn was mainly presented as Mn(III)-EDTA complex. Citrate or EDTA-induced dissolution of birnessite did not decrease the As(III) oxidation rate in the initial stage where As(III) oxidation rate was rapid. Afterwards, As(III) oxidation was conspicuously suppressed in citrate-amended batches, which was mainly attributed to the decrease in adsorption sites by adsorption of citrate/Mn(II)-citrate complex. This suppression was enhanced by the increase in concentrations of dissolved Mn(II). Citrate inhibited As adsorption after As(III) oxidation due to the strong competitive adsorption of citrate/Mn(II)-citrate complex. However, the As(III) oxidation rate was increased in EDTA-amended batches in the late stage, which mainly derived from the increase in the active sites via birnessite dissolution. The strong complexation ability of EDTA led to formation of Mn(III)-EDTA complex. Arsenic adsorption was not affected due to the limited competitive adsorption of the complex on the solid. This work reveals the critical role of low molecular weight organic acids in geochemical behaviors of As and Mn in aqueous environment.

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.

Surprisingly Flexible Oxonium/Borohydride Ion Pair Configurations

We investigate the geometry of oxonium/borohydride ion pairs [ether-H⁽⁺⁾-ether][LA-H^(-)] with dioxane, THF, and Et₂O as ethers and B(C₆F₅)₃ as the Lewis acid (LA). The question is about possible location of the disolvated proton, [ether-H⁽⁺⁾-ether], with respect to the hydride of the structurally complex [LA-H^(-)] anion. Using Born-Oppenheimer molecular dynamics and a comparison of the potential and free energies of the optimized configurations, we show that herein considered ion pairs are much more flexible geometrically than previously thought. Conformers with different locations of cations with respect to anions are governed by a flat energy-landscape. We found a novel configuration in which oxonium is below [LA-H^(-)], with respect to the direction of borane → hydride vector, and the proton-hydride distance is ca. 6 Å. With calculations of the vibrational spectra of [ether-H⁽⁺⁾-ether][(C₆F₅)₃B-H^(-)] for dioxane, THF, and Et₂O as ethers, we investigate the manifestation of SSLB-type (short, strong, low-barrier) hydrogen bonding in the OHO motif of an oxonium cation.