Coordination and ligand exchange dynamics of solvated metal ions

Recent developments in computer speed and capacity have opened the access to highly accurate molecular dynamics simulations based on quantum mechanically calculated forces for the chemically relevant region around ions in solution (QM/MM formalism). This accuracy, although still extremely consuming (30-300 days of CP time per simulation), is needed for reliable structural details and ligand exchange rates. A large number of main group and transition metal ions have been investigated by this approach, giving very detailed insight into the properties of these ions in solution and allowing to classify the ions by various characteristics. Most first-row transition metal ions have a very stable first hexa-coordinated solvation shell, whose vibrational distortions, however, strongly influence the dynamics of the second shell. The dynamical Jahn-Teller effect - shown to be a femto- and picosecond phenomenon - can strongly influence ligand coordination and exchange dynamics. A large number of ions with very labile solvation shell such as most main group ions, but also transition metal ions, e.g. Ag(I) and Hg(II), can change their coordination within the picosecond scale, leading to an almost simultaneous presence of several species hardly accessible by present experimental techniques. Among these ions, the structure breakers are of particular interest, and it could be shown that there are two types of them, one with a large and very labile first coordination shell such as Cs(I), the other characterised by a small first but an unusually large second solvation shell such as Au(I). Investigations of metal ions coordinated to ammonia ligands have shown that coordination to hetero-atoms can accelerate the ligand exchange reaction rates by several orders of magnitude, e.g. for Cu(II) and Ni(II). Simulations of ions in aqueous ammonia gave a very detailed picture of the complexity of species almost simultaneously present and illustrate the enormous difficulties encountered when trying to fit X-ray or neutron diffraction data for such systems. In general, ligand exchange rates situated in the picosecond range are far below the NMR scale, and as femtosecond laser pulse spectroscopy could not be applied so far to ionic solutions, accurate simulations have become a very important tool to access structure and dynamics of solvated ions. A number of VIDEO clips supplied on the Web as supporting material illustrates the processes occurring in solutions of the metal ions.     

Stability constants: a new twist in transition metal bispidine chemistry

Transition metal complexes with 2,4-substituted tetradentate, 2,3,4- and 2,4,7-substituted pentadentate, and 2,3,4,7-substituted hexadentate bispidine ligands (bispidine = 3,7-diazabicyclo[3.3.1]nonane) with two tertiary amine and two, three, or four pyridine donors are relatively stable (10 < log K(CuL) < 18). Interestingly, the two isomeric pentadentate ligands have very different stabilities with a variety of metal ions and, depending on the metal ion, one of the isomers leads to more stable complexes than the hexadentate and the other to less stable complexes than the tetradentate ligand. Another interesting observation is that the complex stabilities of all bispidine ligands reported here do not follow the Iriving-Williams series since the stability constants of the cobalt(II) complexes are up to 4 log units larger than those of the corresponding nickel(II) complexes. All these observations are analyzed on the basis of subtle distortions of the coordination geometries, and these have been related previously to Jahn-Teller-derived distortions for the copper(II) complexes. However, similar but less pronounced structural properties are observed with other metal centers, as shown, e.g., with the experimental structures of the two zinc(II) complexes with the isomeric pentadentate ligands reported here. The structural properties and the related stabilities are also discussed on the basis of force field calculations.     

Functional dynamics of ion channels: modulation of proton movement by conformational switches

Detailed comparative studies of proton relay in native and chemically modified gramicidin channels provide a unique opportunity to uncover the structural basis of biological proton transport. The function of ion channels hinges on their ability to provide surrogate solvation in narrow pore filters so as to overcome the dielectric barrier presented by biological membranes. In the potassium channel KcsA and in the cation channel gramicidin, permeant selectivity and mobility are determined by the proteinaceous matrix via hydrogen bonding, charge-dipole, and dipole-dipole interactions. In particular, main-chain carbonyl groups in these pore interiors play an essential role in the solvation of alkali ions and of protons. In this study, molecular dynamics simulations reveal how the translocation of H(+) is controlled by nanosecond conformational transitions exchanging distorted states of the peptidic backbone in the single-file region of a dioxolane-linked analogue of the gramicidin dimer. These results underline the functional role of channel dynamics and provide a mechanism for the modulation of proton currents by fluctuating dipoles.     

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential

The alkaline earth metals calcium and magnesium are critically involved in many biomolecular processes. To understand the hydration thermodynamics of these ions, we have performed molecular dynamics simulations using a polarizable potential. Particle-mesh Ewald for point multipoles has been applied to the calculation of electrostatic interactions. The parameters in this model have been determined from an ab initio quantum mechanical calculation of dimer interactions between ions and water. Two methods for ion solvation free energy calculation, free energy perturbation, and the Bennett acceptance ratio have been compared. Both predict results consistent with other theoretical estimations while the Bennett approach leads to a much smaller statistical error. Based on the Born theory and the ion-oxygen radial distribution functions, we estimate the effective size of the ions in solution, concluding that K(+) > Na(+) congruent with Ca(2+) > Mg(2+). There appears to be much stronger perturbation in water structure, dynamics, and dipole moment around the divalent cations than the monovalent K(+) and Na(+). The average water coordination numbers for Ca(2+) and Mg(2+) are 7.3 and 6, respectively. The lifetime of water molecules in the first solvation shell of Mg(2+) is on the order of hundreds of picoseconds, in contrast to only few picoseconds for Ca(2+), K(+), or Na(+).     

Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction

Electronic states and solvation of Cu and Ag aqua ions are investigated by comparing the Cu(2+) + e(-)--> Cu(+) and Ag(2+) + e(-)--> Ag(+) redox reactions using density functional-based computational methods. The coordination number of aqueous Cu(2+) is found to fluctuate between 5 and 6 and reduces to 2 for Cu(+), which forms a tightly bound linear dihydrate. Reduction of Ag(2+) changes the coordination number from 5 to 4. The energetics of the oxidation reactions is analyzed by comparing vertical ionization potentials, relaxation energies, and vertical electron affinities. The model is validated by a computation of the free energy of the full redox reaction Ag(2+) + Cu(+) --> Ag(+) + Cu(2+). Investigation of the one-electron states shows that the redox active frontier orbitals are confined to the energy gap between occupied and empty states of the pure solvent and localized on the metal ion hydration complex. The effect of solvent fluctuations on the electronic states is highlighted in a computation of the UV absorption spectrum of Cu(+) and Ag(+).     

Investigation of uranyl nitrate ion pairs complexed with amide ligands using electrospray ionization ion trap mass spectrometry and density functional theory

Ion populations formed from electrospray of uranyl nitrate solutions containing different amides vary depending on ligand nucleophilicity and steric crowding at the metal center. The most abundant species were ion pair complexes having the general formula [UO(2)(NO(3))(amide)(n=2,3)](+); however, singly charged complexes containing the amide conjugate base and reduced uranyl UO(2)(+) were also formed as were several doubly charged species. The formamide experiment produced the greatest diversity of species resulting from weaker amide binding, leading to dissociation and subsequent solvent coordination or metal reduction. Experiments using methyl formamide, dimethyl formamide, acetamide, and methyl acetamide produced ion pair and doubly charged complexes that were more abundant and less abundant complexes containing solvent or reduced uranyl. This pattern is reversed in the dimethylacetamide experiment, which displayed lower abundance doubly charged complexes, but augmented reduced uranyl complexes. DFT investigations of the tris-amide ion pair complexes showed that interligand repulsion distorts the amide ligands out of the uranyl equatorial plane and that complex stabilities do not increase with increasing amide nucleophilicity. Elimination of an amide ligand largely relieves the interligand repulsion, and the remaining amide ligands become closely aligned with the equatorial plane in the structures of the bis-amide ligands. The studies show that the phenomenological distribution of coordination complexes in a metal-ligand electrospray experiment is a function of both ligand nucleophilicity and interligand repulsion and that the latter factor begins exerting influence even in the case of relatively small ligands like the substituted methyl-formamide and methyl-acetamide ligands.     

Alkali metal ion binding to amino acids versus their methyl esters: affinity trends and structural changes in the gas phase

The relative alkali metal ion (M(+)) affinities (binding energies) between seventeen different amino acids (AA) and the corresponding methyl esters (AAOMe) were determined in the gas phase by the kinetic method based on the dissociation of AA-M(+)-AAOMe heterodimers (M=Li, Na, K, Cs). With the exception of proline, the Li(+), Na(+), and K(+) affinities of the other aliphatic amino acids increase in the order AAAAOMe is already observed for K(+). Proline binds more strongly than its methyl ester to all M(+) except Li(+). Ab initio calculations on the M(+) complexes of alanine, beta-aminoisobutyric acid, proline, glycine methyl ester, alanine methyl ester, and proline methyl ester show that their energetically most favorable complexes result from charge solvation, except for proline which forms salt bridges. The most stable mode of charge solvation depends on the ligand (AA or AAOMe) and, for AA, it gradually changes with metal ion size. Esters chelate all M(+) ions through the amine and carbonyl groups. Amino acids coordinate Li(+) and Na(+) ions through the amine and carbonyl groups as well, but K(+) and Cs(+) ions are coordinated by the O atoms of the carboxyl group. Upon consideration of these differences in favored binding geometries, the theoretically derived relative M(+) affinities between aliphatic AA and AAOMe are in good overall agreement with the above given experimental trends. The majority of side chain functionalized amino acids studied show experimentally the affinity order AAAAOMe. The latter ranking is attributed to salt bridge formation.     

Free energy of solvation of simple ions: molecular-dynamics study of solvation of Cl- and Na+ in the ice/water interface

Molecular-dynamics simulations of Cl(-) and Na(+) ions are performed to calculate ionic solvation free energies in both bulk simple point-charge/extended water and ice 1 h at several different temperatures, and at the basal ice 1 h/water interface. For the interface we calculate the free energy of "transfer" of the ions across the ice/water interface. For the ions in bulk water in the NPT ensemble at 298 K and 1 atm, results are found to be in good agreement with experiments, and with other simulation results. Simulations performed in the NVT ensemble are shown to give equivalent solvation free energies, and this ensemble is used for the interfacial simulations. Solvation free energies of Cl(-) and Na(+) ions in ice at 150 K are found to be approximately 30 and approximately 20 kcal mol(-1), respectively, less favorable than for water at room temperature. Near the melting point of the model the solvation of the ions in water is the same (within statistical error) as that measured at room temperature, and in the ice is equivalent and approximately 10 kcal mol(-1) less favorable than the liquid. The free energy of transfer for each ion across ice/water interface is calculated and is in good agreement with the bulk observations for the Cl(-) ion. However, for the model of Na(+) the long-range electrostatic contribution to the free energy was more negative in the ice than the liquid, in contrast with the results observed in the bulk calculations.     

Analyzing coordination preferences of Mg2+ complexes: insights from computational and database study

Solvation of metal cations has attracted substantial interest on account of its functional importance in biological systems. In the present study, we undertake a comprehensive analysis of hydrated complexes of Mg²⁺ with up to 20 water molecules using MP2/cc-pVTZ and density functional theory (DFT) calculations. The effect of first, second, and higher solvation shells on magnesium coordination has been systematically analyzed by considering Mg²⁺(H₂O) _n complexes. Numerous competing conformations for each of the metal ion complexes have been explored and the minima structures obtained were further analyzed. The study probes the relative preferences among various coordination numbers and unambiguously establishes that coordination number 6 is the most optimal choice. The relative abundance of Mg²⁺ ion and its coordination with water and other ligands has been analyzed in the Protein Data Bank and Cambridge Structural Database. It is noted that the M–O distance and charge transfer to metal ion increase as the number of solvating water molecules increases. The computational studies are in excellent agreement with the experimental observations, and provide support to multiple coordinate site preferences for Mg²⁺.     

Mechanisms of ion transport in lithium salt-doped polymeric ionic liquid electrolytes at higher salt concentrations

We used atomistic simulations to study the mechanisms of ion transport in salt-doped polymeric ionic liquid systems at higher salt concentrations. Consistent with the experimental observations, our simulations indicate that at higher salt concentrations, the anion mobilities become lower than that of the lithium cations. Further, the anion mobilities become relatively insensitive to the salt concentration, while the mobilities of lithium increase with increasing salt concentration. We rationalize the results for the anion mobilities by considering the fractions of anions which are exclusively coordinated with the polycations (Type1); co-coordinated with cations and lithium (Type2); and those exclusively coordinated with lithium (Type3). By considering the coordination characteristics of the different types of anions and their hopping motions, we demonstrate that the net anion mobilities results from a compensation effect of the salt concentration dependence of the mobilities of the different anions. With respect to the mobilities of the lithium ions, we demonstrate that the latter moves primarily by a structural diffusion mechanism involving refreshing of the solvation shell during hopping. Further, for the majority of the lithium ions, the solvation shell is shown to be comprised of co-coordinated Type2 anions, and that the number of polycations and the unique polymer chains involved in such coordination decreases with increasing salt concentration. Such changes are shown to weaken the solvation shell around the lithium, thereby facilitating faster ion motion. Together, our results suggest that systems in which the anion which exhibits a stronger coordination to the polycation in comparison to that of the lithium can facilitate higher transference numbers without a concomitant reduction in the mechanical strength.     

A hybrid forces Quantum Mechanical Charge Field Molecular Dynamics of Cs+ ion in aqueous ammonia: A solvation lability, “structure breaking” phenomenon and hydrogen bond properties

The dynamics and structure of Cs⁺ solvation in an aqueous ammonia solution have been investigated using the Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) simulation method. The system contained 18.6% ammonia in aqueous solution at 298.15 K. The QM region was set to a radius of 7.0 Å to include the first and second solvation shells. The Hartree-Fock (HF) level was applied to calculate the ion-ligand and ligand–ligand interactions in the QM region using the LANL2DZ-ECP basis set for the ion and DZP-Dunning for the ligands. The radial distribution revealed only one solvation shell, indicating a labile solvation structure. The various coordination number of ligands suggests an instant exchange between them. The mean residence times of 1.29 and 0.9 ps were less than in the pure water and liquid ammonia system, indicating higher mobility ligands of the aqueous ammonia system. The preferential factor 0.55 supports the hypothesis that the Cs⁺ ion prefers to be dissolved in water. As the ligands moves further away from the ion, the observed number of hydrogen bonds increases, revealing the “structure-breaking” property of the Cs⁺ ion. The minimum angle ligand-ion-ligand tends to be higher near the ion, confirming this phenomenon.     

Coordination and solvation of copper ion: infrared photodissociation spectroscopy of Cu(+)(NH(3))(n) (n = 3-8)

Coordination and solvation structures of the Cu(+)(NH(3))(n) ions with n = 3-8 are studied by infrared photodissociation spectroscopy in the NH-stretch region with the aid of density functional theory calculations. Hydrogen bonding between NH(3) molecules is absent for n = 3, indicating that all NH(3) molecules are bonded directly to Cu(+) in a tri-coordinated form. The first sign of hydrogen bonding is detected at n = 4 through frequency reduction and intensity enhancement of the infrared transitions, implying that at least one NH(3) molecule is placed in the second solvation shell. The spectra of n = 4 and 5 suggest the coexistence of multiple isomers, which have different coordination numbers (2, 3, and 4) or different types of hydrogen-bonding configurations. With increasing n, however, the di-coordinated isomer is of growing importance until becoming predominant at n = 8. These results signify a strong tendency of Cu(+) to adopt the twofold linear coordination, as in the case of Cu(+)(H(2)O)(n).     

A first principles molecular dynamics study of lithium atom solvation in binary liquid mixture of water and ammonia: structural, electronic, and dynamical properties

The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li(+) ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li(+) ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li(+) ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen bonds.     

Infrared spectroscopy of phenylalanine Ag(I) and Zn(II) complexes in the gas phase

Infrared multiple-photon dissociation (IR-MPD) spectroscopy has been applied to singly-charged complexes involving the transition metals Ag(+) and Zn(2+) with the aromatic amino acid phenylalanine. These studies are complemented by DFT calculations. For [Phe+Ag](+) the calculations favor a tridentate charge solvation N/O/ring structure. The experimental spectrum strongly supports this as the predominant binding geometry and, in particular, rules out a significant presence of the salt-bridge conformation. Zn(2+) forms a deprotonated dimer complex with Phe, [Zn+Phe(2)-H](+), in which the +2 oxidation state serves as a useful biomimetic model for zinc protein sites. A number of low-energy conformations were located, of which the lowest-energy conformer predicted by the calculations involves a Phe ligand deprotonated on the carboxylic acid, while the other Phe ligand is in the tridentate charge solvation conformation. The calculated IR spectrum of this conformer gives a close fit to the experimental spectrum, strongly supporting this as the predominant binding geometry. This most stable calculated complex is characterized by N/ O/ring metal chelation with a tetrahedral-type coordination core of Zn(2+) to N and O of both ligands. Another similar tightly chelated structure shows a square-planar-type coordination core, but this structure is computed to be less stable and gives a less satisfactory match to the experimental spectrum. This preference for the tetrahedral geometry of the Lewis-basic atomic ligands parallels the common Zn(II) coordination geometry in proteins. The number of clearly identifiable peaks resolved in the IR-MPD spectra as well as the much-improved matches between the observed spectra and the DFT-calculated spectra of the most stable geometries compared to previous studies are noteworthy for systems of this size and complexity. These results demonstrate that IR spectroscopy of transition metal-amino acid complexes in combination with DFT calculations is a very powerful structural tool, readily applicable to biomimetic systems that model, for example, the reaction centers of proteins in the solvent-free environment. In addition, we present a novel ion-capturing method for Fourier transform ion cyclotron resonance mass spectrometry which removes the necessity of a buffer gas pulse, while allowing ion trapping at moderate voltages with apparently reduced collisional excitation of the ions.     

Dissociation of polyether-transition metal ion dimer complexes in a quadrupole ion trap

The formation and dissociation of dimer complexes consisting of a transition metal ion and two polyether ligands is examined in a quadrupole ion trap mass spectrometer. Reactions of three transition metals (Ni, Cu, Co) with three crown ethers and four acyclic ethers (glymes) are studied. Singly charged species are created from ion-molecule reactions between laser-desorbed monopositive metal ions and the neutral polyethers. Doubly charged complexes are generated from electrospray ionization of solutions containing metal salts and polyethers. For the singly charged complexes, the capability for dimer formation by the ethers is dependent on the number of available coordination sites on the ligand and its ability to fully coordinate the metal ion. For example, 18-crown-6 never forms dimer complexes, but 12-crown-4 readily forms dimers. For the more flexible acyclic ethers, the ligands that have four or more oxygen atoms do not form dimer complexes because the acyclic ligands have sufficient flexibility to wrap around the metal ion and prevent attachment of a second ligand. For the doubly charged complexes, dimers are observed for all of the crown ethers and glymes, thus showing no dependence on the flexibility or number of coordination sites of the polyether. The nonselectivity of dimer formation is attributed to the higher charge density of the doubly charged metal center, resulting in stronger coordination abilities. Collisionally activated dissociation is used to evaluate the structures of the metal-polyether dimer complexes. Radical fragmentation processes are observed for some of the singly charged dimer complexes because these pathways allow the monopositive metal ion to attain a more favorable 2 + oxidation state. These radical losses are observed for the dimer complexes but not for the monomer complexes because the dimer structures have two independent ligands, a feature that enhances the coordination geometry of the complex and allows more flexibility for the rearrangements necessary for loss of radical species. Dissociation of the doubly charged complexes generated by electrospray ionization does not result in losses of radical neutrals because the metal ions already exist in favorable 2+ oxidation states.     

Thermodynamics of complex formation in dimethyl sulfoxide with ligands coordinating via N,P, As,Sb, OR Bi : III. A comparison between aromatic and aliphatic amines and phosphines

The stabilities of the complexes formed by silver(I), cadmium(II) and zinc(II) with tri-n-butylamine and tri-n-butylphosphine have been determined in dimethyl sulfoxide (DMSO). For the two latter metal ions, it has also been found that complexes are not formed in appreciable amounts with the triphenyl compounds Ph₃X, X = N, P and, in the case of cadmium(II), also As.From these and earlier measurements referring to DMSO as well as aqueous solutions, it was found that the stepwise stability constants increase by roughly one power of ten for each aromatic ring replaced by an aliphatic group, evidently as a consequence of the improved donor properties of the coordinating atoms. Further, for ligands of the same type, the stabilities are always markedly lower in DMSO than in aqueous solution. This is certainly due to the fact that the solvent molecules compete more strongly for the coordination sites in DMSO than in water, as reflected by the larger heats of solvation found in the former solvent for the metal ions concerned.     

Coordination chemistry of a new rigid, hexadentate bispidine-based bis(amine)tetrakis(pyridine) ligand

The hexadentate bispidine-based ligand 2,4-bis(2-pyridyl)-3,7-bis(2-methylenepyridine)-3,7-diazabicyclo[3.3.1]nonane-9-on-1,5-bis(carbonic acid methyl ester), L(6m), with four pyridine and two tertiary amine donors, based on a very rigid diazaadamantane-derived backbone, is coordinated to a range of metal ions. On the basis of experimental and computed structural data, the ligand is predicted to form very stable complexes. Force field calculations indicate that short metal-donor distances lead to a buildup of strain in the ligand; that is, the coordination of large metal ions is preferred. This is confirmed by experimentally determined stability constants, which indicate that, in general, stabilities comparable to those with macrocyclic ligands are obtained with the relative order Cu(2+) > Zn(2+) > Ni(2+) < Co(2+), which is not the typical Irving-Williams behavior. The preference for large M-N distances also emerges from relatively high redox potentials (the higher oxidation states, that is, the smaller metal ions, are destabilized) and from relatively weak ligand fields (dd-transition, high-spin electronic ground states). The potentiometric titrations confirm the efficient encapsulation of the metal ions since only 1:1 complexes are observed, and, over a large pH range, ML is generally the only species present in solution.     

Metallosurfactants of bioinorganic interest: Coordination-induced self assembly

This review covers selected surfactant ligands that undergo a change in aggregate morphology upon coordination of a metal ion, with a particular focus on coordination-induced micelle-to-vesicle transitions. The surfactants include microbially produced amphiphilic siderophores, as well as synthetic amphiphilic ligands. The mechanism of the metal-induced phase change is considered in light of the coordination chemistry of the metal ions, the nature of the ligands, and changes in molecular geometry that result from metal coordination. Of particular interest are biologically produced amphiphiles that coordinate transition metal ions and amphiphilic ligands of relevance to bioinorganic chemistry.     

Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A<Subscript>2A</Subscript> adenosine receptor orthosteric binding site using a molecular docking approach? Insights from <Emphasis Type="Italic">Dockbench</Emphasis>

The allosteric modulation of G protein-coupled receptors (GPCRs) by sodium ions has received considerable attention as crystal structures of several receptors, in their inactive conformation, show a Na⁺ ion bound to specific residues which, in the human A_2A adenosine receptor (hA_2A AR), are Ser91^3.39, Trp246^6.48, Asn280^7.45, and Asn284^7.49. A cluster of water molecules completes the coordination of the sodium ion in the putative allosteric site. It is absolutely consolidated that the progress made in the field of GPCRs structural determination has increased the adoption of docking-driven approaches for the identification or the optimization of novel potent and selective ligands. Despite the extensive use of docking protocols in virtual screening approaches, to date, almost any of these studies have been carried out without taking into account the presence of the sodium cation and its first solvation shell in the putative allosteric binding site. In this study, we have focused our attention on determining how the presence of sodium ion binding and additionally its first hydration sphere, in hA_2AAR could influence the ligand positioning accuracy during molecular docking simulations for most of the available resting and activated hA_2A AR crystal structures, using DockBench as a comparative benchmarking tool and implementing a new correlation coefficient (EM). This work provides indications on the evidence that the posing performance (accuracy and/or precision) of the docking protocols in reproducing the crystallographic poses of different hA_2A AR antagonists is generally increased in the presence of the sodium cation and its first solvation shell, in agreement with experimental observations. Consequently, the inclusion of sodium ion and its first solvation shell should be considered in order to facilitate the selection of new potential ligands in all molecular docking-based virtual screening protocols that aim to find novel GPCRs antagonists and inverse agonists.     

Molecular simulation study of temperature effect on ionic hydration in carbon nanotubes

Molecular dynamics simulations have been performed to investigate the hydration of Li(+), Na(+), K(+), F(-), and Cl(-) inside the carbon nanotubes at temperatures ranging from 298 to 683 K. The structural characteristics of the coordination shells of ions are studied, including the ion-oxygen radial distribution functions, the coordination numbers, and the orientation distributions of the water molecules. Simulation results show that the first coordination shells of the five ions still exist in the nanoscale confinement. Nevertheless, the first coordination shell structures of cations change more significantly than those of anions because of the preferential orientation of the water molecules induced by the carbon nanotube. The first coordination shells of cations are considerably less ordered in the nanotube than in the bulk solution, whereas the change of the first coordination shell structures of the anions is minor. Furthermore, the confinement induces the anomalous behavior of the coordination shells of the ions with temperature. The first coordination shell of K(+) are found to be more ordered as the temperature increases only in the carbon nanotube with the effective diameter of 1.0 nm, implying the enhancement of the ionic hydration with temperature. This is contrary to that in the bulk solution. The coordination shells of the other four ions do not have such behavior in the carbon nanotube with the effective diameter ranging from 0.73 to 1.00 nm. The easier distortion of the coordination shell of K(+) and the match of the shell size and the nanotube size may play roles in this phenomenon. The exchange of water molecules in the first coordination shells of the ions with the solution and the ion diffusion along the axial direction of the nanotube are also investigated. The mobility of the ions and the stability of the coordination shells are greatly affected by the temperature in the nanotube as in the bulk solutions. These results help to understand the biological and chemical processes at the high temperature.