1D-RISM study of glycine zwitterion hydration and ion-molecular complex formation in aqueous NaCl solutions

Cation-Binding of Glutamate in Aqueous Solution

Interactions of the cations Li+, Na+, Mg2+, and Ca2+ with L-glutamate (Glu-) in aqueous solution were studied at room temperature with dielectric relaxation spectroscopy in the gigahertz region. Spectra of ∼0.4 M NaGlu with added LiCl, NaCl, MgCl2, or CaCl2 (c(MCln) ≤ 1.5 M) were evaluated and experiments supplemented by density functional theory and 3D reference interaction site model (3D-RISM) calculations. In addition to the modes found for aqueous NaGlu, namely, the reorientation of free Glu- ions (peaking at ∼1.6 GHz), of moderately retarded H2O molecules hydrating the carboxylate moieties of Glu- (∼8.4 GHz), of the cooperative resettling of the H-bond network of bulk water (∼20 GHz), and its preceding fast H-bond flip (∼400 GHz), an additional low-frequency relaxation at ∼0.4 GHz was detected upon the addition of the four salts. In the case of NaGlu + MgCl2(aq) and NaGlu + CaCl2(aq), this mode could be unequivocally assigned to an ion pair formed by the cation and the side-chain carboxylate moiety of Glu-. For NaGlu + LiCl(aq), either this species or a backbone-[Li+-H2O-Cl--Glu-] triple ion is formed. Binding constants increase in the order Li+ Collapse

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Grants

• Fonds der Chemischen Industrie
• G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences

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Affiliation(s)

Sergej Friesen Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg D-93040, Germany
Sergey E. Kruchinin G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya st. 1, Ivanovo 153045, Russian Federation
Marina V. Fedotova G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya st. 1, Ivanovo 153045, Russian Federation
Richard Buchner Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg D-93040, Germany

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Specific Proton-Donor Properties of Glycine Betaine. Metric Parameters and Enthalpy of Noncovalent Interactions in its Dimer, Water Complexes and Crystalline Hydrate

Trimethylglycine (glycine betaine, GB) is an important organic osmolyte that accumulates in various plant species in response to environmental stresses and has significant potential as a bioactive agent with low environmental impact. It is assumed that the hydration of GB is playing an important role in the protective mechanism. The hydration and aggregation properties of GB have not yet been studied in detail at the atomistic level. In this work, noncovalent interactions in the GB dimer and its complexes with water and crystalline monohydrate are studied. Depending on the object, periodic and non-periodic DFT calculations are used. Particular attention is paid to the metric parameters and enthalpies of intermolecular hydrogen bonds. The identification of noncovalent interactions is carried out by means of the Bader analysis of periodic or non-periodic electron density. The enthalpy of hydrogen bonds is estimated using the Rosenberg formula (PCCP 2 (2000) 2699). The specific proton donor properties of glycine betaine are due to its ability to form intermolecular C-H∙∙∙O bonds with the oxygen atom of a water molecule or the carboxylate group of a neighboring GB. The enthalpy of these bonds can be significantly greater than 10 kJ/mol. The water molecule that forms a hydrogen bond with the carboxylate group of GB also interacts with its CH groups through lone pairs of electrons. The C-H∙∙∙O bonds contribute up to 40% of the total entropy of the GB-water interaction, which is about 45 kJ/mol. The possibility of identifying C-H∙∙∙O bonds by the proton nuclear magnetic resonance method is discussed.

Diclofenac Ion Hydration: Experimental and Theoretical Search for Anion Pairs

Self-assembly of organic ions in aqueous solutions is a hot topic at the present time, and substances that are well-soluble in water are usually studied. In this work, aqueous solutions of sodium diclofenac are investigated, which, like most medicinal compounds, is poorly soluble in water. Classical MD modeling of an aqueous solution of diclofenac sodium showed equilibrium between the hydrated anion and the hydrated dimer of the diclofenac anion. The assignment and interpretation of the bands in the UV, NIR, and IR spectra are based on DFT calculations in the discrete-continuum approximation. It has been shown that the combined use of spectroscopic methods in various frequency ranges with classical MD simulations and DFT calculations provides valuable information on the association processes of medical compounds in aqueous solutions. Additionally, such a combined application of experimental and calculation methods allowed us to put forward a hypothesis about the mechanism of the effect of diclofenac sodium in high dilutions on a solution of diclofenac sodium.

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.

Ion Pairing of the Neurotransmitters Acetylcholine and Glutamate in Aqueous Solutions

Neurotransmitters (NTs) play an important role in neural communication, regulating a variety of functions such as motivation, learning, memory, and muscle contraction. Their intermolecular interactions in biological media are an important factor affecting their biological activity. However, the available information on the features of these interactions is scarce and contradictory, especially, in an estimation of possible ion binding. In this paper, we present the results of a study for two well-known NTs, acetylcholine (ACh) and glutamate (Glu), with relation to the NT-inorganic ion and the NT-NT binding in a water environment. The features of NT pairing are investigated in aqueous AChCl and NaGlu solutions over a wide concentration range using the integral equation method in 1D- and 3D- reference interaction site model (RISM) approaches. The data for ACh are given for its two bioactive TG (trans, gauche) and TT (trans, trans) conformers. As was found, for both NTs, the results indicate the NT-inorganic counterion contact pair to be the predominant associate type in the concentrated solutions. In this case, the counterions occupy the vacated "water" space in the hydration shell of the onium moiety (ACh) or carboxylate groups (Glu). For ACh, the "unfolded" TT conformer demonstrates a slightly greater possibility for counterion pairing in comparison with the "folded" TG conformer. For Glu, the probability of its binding with a counterion is slightly stronger for the "side-chain" carboxylate group than for the "backbone" group. The obtained results also revealed an insignificant probability of Glu^--Glu^- pairing. Namely, the RISM data indicate Glu^--Glu^- binding by NH₃⁺-COO^- interactions. A link between the ion binding of NTs and their biological activity is discussed. This contribution adds new knowledge to our understanding of the interactions between the NTs and their molecular environment, providing further insights into the behavior of these compounds in biological media.

Statistical field theory of ion–molecular solutions

Schematic representation of the multipolar molecule surrounded by salt ions in a dielectric solvent medium.

Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac

Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO₂^-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO₂^- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO₂^- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO₂^- group of bioactive molecules with the water molecules in dilute aqueous solutions.

Hydration structure of osmolyte TMAO: concentration/pressure-induced response

The effect of solute concentration/pressure on the TMAO hydration structure was studied to understand its protective action under abiotic stressors.

Evidence for cooperative Na+ and Cl− binding by strongly hydrated l-proline

Strongly hydrated l-proline cooperatively binds Na⁺ and Cl⁻ ions in aqueous solution.

Mobility and association of ions in aqueous solutions: the case of imidazolium based ionic liquids

Combining MD simulations and RISM calculations with experiments, we demonstrated that the interionic interactions of investigated ILs as model 1,1 electrolytes in water solutions are weak but evidently dependent on the molecular structure.

Characterization of selective binding of biologically relevant inorganic ions with the proline zwitterion by 3D-RISM theory

The features of selective binding of several biologically relevant mono- and divalent inorganic ions with the proline zwitterion were studied over a wide range of electrolyte concentrations.