Car-Parrinello MD simulations for the Na+ -phenylalanine complex in aqueous solution

Car-Parrinello molecular dynamics (CPMD) calculations are presented for a Na (+)(Phe) complex in aqueous solution and for various stable Na (+)(Phe) complexes and Na (+)(H 2O) n clusters in the gas phase (with up to six water molecules). The CPMD results are compared to available experimental and ab initio reference data, to DFT results obtained with various combinations of density functionals and basis sets, and to previous classical mechanics MD simulations. The agreement with the reference data in the gas phase validates the CPMD method, showing that it is a valid approach for studying these systems and that it describes correctly the competing Na (+)-Phe and Na (+)-H 2O interactions. Analysis of MD trajectories reveals that the Na (+)(Phe) complex in aqueous solution maintains a stable configuration in which the Na (+) cation hovers above the phenyl ring, at an average distance of 3.85 A from the ring center, while remaining strongly bound to one of the carboxylic oxygens of Phe. Constrained MD simulations indicate that the free energy barrier opposing dissociation of the complex exceeds 5.5 kcal/mol. We thus confirm that "cation- pi" interactions between alcali cations and the pi ring, combined with other kinds of interactions, may allow aromatic amino acids to overcome the competition with water in binding a cation.     

Evidence for the cation-pi interaction between Cu2+ and tryptophan

The cation-pi interaction, a noncovalent interaction of electrostatic nature between a cation and an electron-rich pi system, is increasingly recognized as an important force that influences the structures and functions of molecules including proteins. Unlike other metal cations, the transition metal cation Cu2+ is not regarded to take part in a cation-pi interaction because Cu2+ tends to oxidize the pi electron system, in particular that of Trp, and to introduce covalency in the metal-pi electron interaction. This paper reports the first spectral evidence for the cation-pi interaction between Cu2+ and Trp. The Cu2+ ion bound to the amino N-terminal Cu2+/Ni2+ binding motif composed of three amino acid residues interacts with the indole ring of the fourth Trp residue in a noncovalent manner. The Cu2+-Trp interaction produces a distinct negative band at 223 nm in circular dichroism (CD), which disappears upon mutation or depletion of the Trp residue or upon replacement of the Cu2+ ion by Ni2+. In UV absorption, a pair of negative/positive intensity changes is generated at 222/231 nm by the Cu2+-Trp interaction, being consistent with the previous observations on the indole ring interacting with K+ or a cationic His imidazole ring. The negative CD band around 223 nm is characteristic of the Cu2+-Trp pair and may be useful as a marker of the Cu2+-Trp cation-pi interaction. Coordination of negatively charged ligands to Cu2+ is suggested to be important for the cation to be involved in a cation-pi interaction.     

A Monte Carlo simulation of Fe2+ aqueous solvation

A Monte Carlo simulation of Fe²⁺ aqueous solvation, at 298 K, including 100 water molecules, has been done using periodic boundary conditions under the minimum image conversion. The energy has been calculated in the pair-potential approach, employing the MCY potential for the H₂OH₂O interaction and an ab initio analytical potential generated by us for the Fe²⁺H₂O interaction. The examination of interaction energies and of the radial distribution functions clearly show that the first hydration shell is formed by eight water molecules. By classifying the generated configurations into different significant structures of the solvent, it has been found that the eight water molecules of the first hydration shell are situated in a lightly distorted D_4d structure which maximizes the water—solute stabilization and minimizes the water—water repulsion. Finally, the validity of our theoretical predictions is discussed.     

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.     

Simple cation-pi interaction between a phenyl ring and a protonated amine stabilizes an alpha-helix in water

Cation-pi interactions have been proposed to be important contributors to protein structure and function. In particular, these interactions have been suggested to provide significant stability at the solvent-exposed surface of a protein. We have investigated the magnitude of cation-pi interactions between phenylalanine (Phe) and lysine (Lys), ornithine (Orn), and diaminobutanoic acid (Dab) in the context of an alpha-helix and have found that only the Phe...Orn interaction provides significant stability to the helix, stabilizing it by -0.4 kcal/mol. This interaction energy is in the same range as a salt bridge in an alpha-helix, and equivalent to the recently reported Trp...Arg interaction in an alpha-helix, despite the fact that Trp...guanidinium interactions have been proposed to be stronger than Phe...ammonium interactions. These results indicate that even the simplest cation-pi interaction can provide significant stability to protein structure and demonstrate the subtle factors that can influence the observed interaction energies in designed systems.     

Nuclear magnetic relaxation and ionic solvation of23Na+ and81Br− in aqueous mixtures of simple amides

Ion-solvent interactions of Na⁺ and Br^– in binary aqueous mixtures of formamide,N-methylformamide (NMF), andN,N-dimethylformamide (DMF) are studied by use of²³Na and⁸¹Br magnetic relaxation times, extrapolated to zero salt concentration. The relaxation times, which are controlled by quadrupolar interaction, have been measured over the complete mixture range and are compared with a simplified theoretical formula. It turned out that the²³Na⁺ relaxation in H₂O-formamide and H₂O-NMF mixtures is in excellent agreement with theoretical predictions, implying nonpreferential solvation of Na⁺ in these systems. Small deviations of experimental from theoretical results in H₂O+DMF possibly indicate weak selective hydration of the cation. In the case of the anionic nuclei⁸¹Br^–, deviations from the theoretical curve occur which are to be expected, especially for systems where hydrophobic effects play a role. On the other hand, it is demonstrated that these deviations can easily be explained within the electrostatic theory by differences in structural details of the anionic solvation sphere in the mixtures compared to the pure solvents.     

Molecular simulation studies on the interaction between different polymers in aqueous solution

A molecular dynamics simulation was performed to investigate the aggregates of mixing and the interaction between different polymers in aqueous solution. These polymers include partially hydrolyzed polyacryamide (HPAM), hydroxyethylcellulose (HEC) and polyvinylpyrrolidone (PVP). The structures of mixed aggregates were analyzed from the dihedral angle distribution of: (1) pure HPAM; (2) HPAM in aqueous solution; (3) HPAM with small segments of PVP or HEC in aqueous solution. At the same time, the simulated IR spectra and the calculated interaction parameters were used to distinguish the different interactions between HPAM and PVP or HEC. In order to confirm the validity of the simulated predictions, experimental IR spectra of polymer systems were made, and the specific viscosity of the HPAM and PVP or HEC system was measured using capillary viscometry. It can be seen from the viscosity measurements that the viscosity of the HPAM/PVP system in aqueous solution decreases linearly with an increase in concentration of PVP, whereas a maximum viscosity value appears with the increase in concentration of HEC in the HPAM/HEC system. The conclusion was drawn that the interaction between HPAM and HEC is stronger than the one between HPAM and PVP, and that molecular simulation can be considered as an adjunct to experiments and can provide otherwise inaccessible (or, not easily accessible) microscopic information that experimentalists can use.     

Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited

The solvation and transport of the hydrated excess proton is studied using the Car-Parrinello molecular-dynamics (CPMD) simulation method. The simulations were performed using BLYP and HCTH gradient-corrected exchange-correlation energy functionals. The fictitious electronic mass was chosen to be small enough so that the underlying water structural and dynamical properties were converged with respect to this important CPMD simulation parameter. An unphysical overstructuring of liquid water in the CPMD simulations using the BLYP functional resulted in the formation of long-lived hydrogen-bonding structures involving the excess proton and a particular (special) water oxygen. The excess proton was observed to be attracted to the special oxygen through the entire length of the BLYP CPMD simulations. Consequently, the excess proton diffusion was limited by the mobility of the special oxygen in the slowly diffusing water network and, in turn, the excess proton self-diffusion coefficient was found to be significantly below the experimental value. On the other hand, the structural properties of liquid water in the HCTH CPMD simulation were seen to be in better agreement with experiment, although the water and excess proton diffusions were still well below the experimental value.     

The role of the counteranion in the cation-pi interaction

Chemical double mutant cycles have been used to quantify cation-pi interactions in chloroform as a function of the nature of the counteranion. The cation-pi interaction is -2.5 +/- 0.4 kJ mol(-1) and independent of the anion, even though the overall stability of the complexes varies by an order of magnitude due to competition of the anion for alternative binding sites.     

Ab initio copper–water interaction potential for the simulation of aqueous solutions

A new ab initio effective two-body potential that aims at mimicking the average copper–water interaction energy of the first solvation shell was developed. This new potential, together with the MCY water–water potential and a three-body ion–water–water induction potential, is tested in simulations of gas-phase clusters [Cu²⁺? (H₂O)₂₀] and diluted solutions [Cu²⁺? (H₂O)₂₀₀] at T = 298 K. The results of simulations with conventional ab initio pair potentials, with and without three-body induction corrections, are also presented. The different types of copper–water interaction potentials are evaluated comparatively and the efficiency of the newly proposed effective pair potential is discussed. © 1993 John Wiley & Sons, Inc.     

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.     

Ion solvation in aqueous supercritical electrolyte solutions at finite concentrations: a computer simulation study

A series of results from computer simulations of sodium chloride ionic solutions at both supercritical and ambient conditions are presented. We considered infinite dilute and finite concentration solutions (m=1, 2, 4 mol kg⁻¹) at variable densities. Structure of water around ionic species is carefully analyzed. Special attention is devoted to the effects of ion pairing and clustering. Running coordination numbers and residence times of water molecules are also reported     

Ultrafast electron dynamics at ice-metal interfaces: competition between heterogeneous electron transfer and solvation

Microscopic insight into heterogeneous electron transfer requires an understanding of the participating donor and acceptor states and of their respective interaction. In the regime of strong electronic coupling, two limits have been discussed where either the states overlap directly or the states are separated by a potential barrier. In both situations, the transfer probability is determined by the magnitude of the wave function overlap, whereby in the case of the potential barrier, its width and height are rate limiting. In our study, we observe a dynamical crossover between these two regimes by investigating the electron-transfer dynamics of localized, solvated electrons at ice-metal interfaces. Employing femtosecond time-resolved two-photon photoelectron spectroscopy, we analyze the population dynamics of excess electrons in the ice layer, which experience the competing processes of transfer to the metal electrode and energetic stabilization in the ice by molecular reorientation. Comparing the dynamics of D(2)O on Cu(111) and Ru(001), we observe an early regime at t < 300 fs, where the transfer time is determined by wave-function overlap with the metal and a second regime (t > 300 fs), where the transfer proceeds nearly independent of the substrate. The assignment of these two regimes to the established mechanisms of electron transfer is backed by an empirical model calculation that reproduces the experimental data in an excellent manner.     

Mechanism of interaction between hydroxypropyl cellulose and water in aqueous solutions: Importance of polymer chain length

The utilization of hydroxypropyl cellulose (HPC) can be regarded as unexpected with regard to certain applications, such as being employed as a solubility enhancer for poorly soluble drugs and as a solubilizing agent for nano-suspensions and amorphous solid dispersions. However, the best results were obtained for low-molecular weight (M_w) HPC grades with a short-chain structure. Therefore, in this study, seven grades of HPC with different polymer chain lengths (M_w) are analyzed in various aqueous solutions by a combination of ¹H quantitative NMR spectroscopy, diffusion NMR spectroscopy, and water ligand observed via gradient spectroscopy; these investigations provide insights into the remarkable solubilizing property of HPC at the molecular and supramolecular levels. Furthermore, the hydration and the water residence time are found to be strongly dependent on the polymer chain length of HPC. The quantitative results obtained herein indicate that HPCs with shorter chain lengths retain smaller amounts of water around their hydrated molecules, as compared to their counterparts with longer chain lengths.     

Origin of the high affinity and selectivity of novel receptors for NH4+ over K+: charged hydrogen bonds vs cation-pi interaction

[structure: see text]Given the recent report of a novel pyrazole receptor exhibiting a high selectivity for NH4+ over K+, it would be interesting to investigate the origin of this selectivity and affinity so that better receptors could be designed. On the basis of extensive theoretical studies, we conclude that the origin arises from a subtle interplay of charged H-bonds and cation-pi interactions. The approach employed herein would be very useful in the rational design of novel functional molecular systems.     

Stability of complex of Na+ with 18-crown-6 in nitrobenzene saturated with water

From extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium Na⁺(aq)+HL⁺(nb)⇆NaL⁺(nb)+H⁺(aq) taking place in the two-phase water-nitrobenzene system (L=18-crown-6; aq=aqueous phase, nb=nitrobenzene phase) was evaluated as logK _ex (Na⁺,HL⁺)=0.1. Further, the stability constant of the 18-crown-6-sodium complex in nitrobenzene saturated with water was calculated: logβ _nh(NaL⁺)=8.0.