Cation-Binding of Glutamate in Aqueous Solution.

Interactions of the cations Li, Na, Mg, and Ca 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, MgCl, or CaCl ((MCl) ≤ 1.

The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands.

Viruses are the most numerous biological form living in any ecosystem. Viral diseases affect not only people but also representatives of fauna and flora. The latest pandemic has shown how important it is for the scientific community to respond quickly to the challenge, including critically assessing the viral threat and developing appropriate measures to counter this threat.

Protein 3D Hydration: A Case of Bovine Pancreatic Trypsin Inhibitor.

Characterization of the hydrated state of a protein is crucial for understanding its structural stability and function. In the present study, we have investigated the 3D hydration structure of the protein BPTI (bovine pancreatic trypsin inhibitor) by molecular dynamics (MD) and the integral equation method in the three-dimensional reference interaction site model (3D-RISM) approach. Both methods have found a well-defined hydration layer around the protein and revealed the localization of BPTI buried water molecules corresponding to the X-ray crystallography data.

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.

Hydration and counterion binding of aqueous acetylcholine chloride and carbamoylcholine chloride.

The hydration and Cl ion binding of the neurotransmitter acetylcholine (ACh) and its synthetic analogue, carbamoylcholine (CCh), were studied by combining dilute-solution conductivity measurements with dielectric relaxation spectroscopy and statistical mechanics calculations at 1D-RISM and 3D-RISM level. Chloride ion binding was found to be weak but not negligible. From the ∼30 water molecules coordinating ACh and CCh only ∼1/3 is affected in its rotational dynamics by the cation, with the majority - situated close to the hydrophobic moieties - only retarded by a factor of ∼2.

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.

Renormalized site density functional theory for models of ion hydration.

The development of accurate statistical mechanics models of molecular liquid systems is a problem of great practical and fundamental importance. Site-density functional theory (SDFT) is one of the promising directions in this area, but its success hinges upon the ability to efficiently reconcile the co-existence of two distinct intra- and inter-molecular interaction regimes in a molecular liquid. The renormalized formulation of SDFT (RSDFT), which we have recently developed, resolves this problem by introducing an additional potential field variable that decouples two interaction scales and maps the molecular liquid problem onto the effective simple liquid mixture.

Hydration and dynamics of L-glutamate ion in aqueous solution.

Aqueous solutions of sodium l-glutamate (NaGlu) in the concentration range 0 < c/M ≤ 1.90 at 25 °C were investigated by dielectric relaxation spectroscopy (DRS) and statistical mechanics (1D-RISM and 3D-RISM calculations) to study the hydration and dynamics of the l-glutamate (Glu-) anion. Although at c → 0 water molecules beyond the first hydration shell are dynamically affected, Glu- hydration is rather fragile and for c ⪆ 0.

Chemical bond effects in classical site density functional theory of inhomogeneous molecular liquids.

Intra-molecular interactions or chemical bonds represent one of the main distinguishing characteristics of molecular fluids. Development of accurate and practical methods to treat these effects is one of the long standing problems in classical site density functional theory (SDFT). One particular instance when these issues become particularly severe is the case of classical interaction potentials with auxiliary sites or dummy atoms.

Hydration and ion association of aqueous choline chloride and chlorocholine chloride.

The choline ion (Ch) is ubiquitous in nature and also its synthetic homologue, chlorocholine (ClCh), is widely used. Nevertheless, surprisingly little information on the hydration and counter-ion binding of these cations can be found in the literature. In this contribution we report effective hydration numbers, determined by dielectric relaxation spectroscopy, and ion-pair association constants with Cl, determined by dilute-solution conductivity measurements.

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

In nature the amino acid l-proline (Pro) is a ubiquitous and highly effective osmolyte protecting cells against osmotic stress. To understand this effect knowledge of the hydration of Pro and its interactions with dissolved salts is essential. We studied these properties by combining statistical mechanics and broadband dielectric spectroscopy and found that Pro remains strongly hydrated up to high amino-acid concentrations.

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

The mobility and the mechanism of ion pairing of 1,1 electrolytes in aqueous solutions were investigated systematically on nine imidazolium based ionic liquids (ILs) from 1-methylimidazolium chloride, [MIM][Cl], to 1-dodecyl-3-methylimidazolium chloride, [1,3-DoMIM][Cl], with two isomers 1,2-dimethylimidazolium chloride, [1,2-MMIM][Cl], and 1,3-dimethylimidazolium chloride, [1,3-MMIM][Cl]. Molecular dynamics (MD) simulations, statistical mechanics calculations in the framework of the integral equation theory using one-dimensional (1D-) and three-dimensional (3D-) reference interaction site model (RISM) approaches as well as conductivity measurements were applied. From experiment and MD simulations it was found that the mobility/diffusion coefficients of cations in the limit of infinite dilution decrease with an increasing length of the cation alkyl chain, but not linearly.

Proline hydration at low temperatures: its role in the protection of cell from freeze-induced stress.

The natural amino acid L-α-proline (Pro) is a compatible osmolyte which accumulates in the cell cytoplasm to protect structure and function of various proteins and enzymes under abiotic stress, like for instance, freezing. It is assumed that the interactions of Pro with intracellular water play an important role in the protection mechanism. However, until now the details of these interactions are far from being fully understood.

Hydration and Ion Binding of the Osmolyte Ectoine.

Ectoine is a widespread osmolyte enabling halophilic bacteria to withstand high osmotic stress that has many potential applications ranging from cosmetics to its use as a therapeutic agent. In this contribution, combining experiment and theory, the hydration and ion-binding of this zwitterionic compound was studied to gain information on the functioning of ectoine in particular and of osmolytes in general. Dielectric relaxation spectroscopy was used to determine the effective hydration number of ectoine and its effective dipole moment in aqueous solutions with and without added NaCl.

Ion-selective interactions of biologically relevant inorganic ions with alanine zwitterion: a 3D-RISM study.

The ion-molecular association between inorganic ions and the charged groups of alanine zwitterion in biologically relevant aqueous salt solutions, namely NaCl(aq), KCl(aq), MgCl2(aq), and CaCl2(aq), has been investigated over a wide range of electrolyte concentration. The influence of salt concentration on the stability of the formed ion-molecular associates is analyzed. The structure of the formed aggregates and its dependence on salt concentration and chemical nature of the inorganic ion are discussed.

Ion-binding of glycine zwitterion with inorganic ions in biologically relevant aqueous electrolyte solutions.

The ion-binding between inorganic ions and charged functional groups of glycine zwitter-ion in NaCl(aq), KCl(aq), MgCl2(aq), and CaCl2(aq) has been investigated over a wide salt concentration range by using integral equation theory in the 3D-RISM approach. These systems mimic biological systems where binding of ions to charged residues at protein surfaces is relevant. It has been found that the stability of ion pairs formed by the carboxylate group and added inorganic cations decreases in the sequence Mg(2+)>Ca(2+)>Na(+)>K(+).

Integral Equation Theory of Molecular Solvation Coupled with Quantum Mechanical/Molecular Mechanics Method in NWChem Package.

We have developed a hybrid approach based on a combination of integral equation theory of molecular liquids and quantum mechanical/molecular mechanics (QM/MM) methodology in NorthWest computational Chemistry (NWChem) software package. We have split the evaluations into consequent QM/MM and statistical mechanics calculations based on the one-dimensional reference interaction site model, which allows us to reduce significantly the time of computation. The method complements QM/MM capabilities existing in the NWChem package.