Photometric reagents for alkali metal ions, based on crown-ether complex formation--III. 4'-picrylaminobenzo-15-crown-5 derivatives

An extraction study of alkali metal cations has been made with crown-ether reagents, 4'-picrylaminobenzo-15-crown-5 derivatives (HL). On dissociation in alkaline medium, the orange HL gives the blood-red anion L(-) and extracts alkali metal ions into chloroform as coloured complexes of composition ML.HL or ML. The ease of extraction decreases in the order, K(+) > Rb(+) > Cs(+) > Na(+) > Li(+). The extracted complexes are ML.HL for K(+) and Rb(+), and both ML.HL and ML for Na(+). The Li(+) complex is not extracted. The photometric determination of 10-800 ppm of K(+) is possible in the presence of other alkali and alkaline earth metal ions.     

A solid-state 23Na NMR study of monovalent cation binding to double-stranded DNA at low relative humidity

We report a solid-state (23)Na NMR study of monovalent cation (Li(+), Na(+), K(+), Rb(+), Cs(+) and NH(4) (+)) binding to double-stranded calf thymus DNA (CT DNA) at low relative humidity, ca 0-10%. Results from (23)Na--(31)P rotational echo double resonance (REDOR) NMR experiments firmly establish that, at low relative humidity, monovalent cations are directly bound to the phosphate group of CT DNA and are partially dehydrated. On the basis of solid-state (23)Na NMR titration experiments, we obtain quantitative thermodynamic parameters concerning the cation-binding affinity for the phosphate group of CT DNA. The free energy difference (DeltaG degrees ) between M(+) and Na(+) ions is as follows: Li(+) (-1.0 kcal mol(-1)), K(+) (7.2 kcal mol(-1)), NH(4) (+) (1.0 kcal mol(-1)), Rb(+) (4.5 kcal mol(-1)) and Cs(+) (1.5 kcal mol(-1)). These results suggest that, at low relative humidity, the binding affinity of monovalent cations for the phosphate group of CT DNA follows the order: Li(+) > Na(+) > NH(4) (+) > Cs(+) > Rb(+) > K(+). This sequence is drastically different from that observed for CT DNA in solution. This discrepancy is attributed to the different modes of cation binding in dry and wet states of DNA. In the wet state of DNA, cations are fully hydrated. Our results suggest that the free energy balance between direct cation-phosphate contact and dehydration interactions is important. The reported experimental results on relative ion-binding affinity for the DNA backbone may be used for testing theoretical treatment of cation-phosphate interactions in DNA.     

UV and IR spectroscopic studies of cold alkali metal ion-crown ether complexes in the gas phase

We report UV photodissociation (UVPD) and IR-UV double-resonance spectra of dibenzo-18-crown-6 (DB18C6) complexes with alkali metal ions (Li(+), Na(+), K(+), Rb(+), and Cs(+)) in a cold, 22-pole ion trap. All the complexes show a number of vibronically resolved UV bands in the 36,000-38,000 cm(-1) region. The Li(+) and Na(+) complexes each exhibit two stable conformations in the cold ion trap (as verified by IR-UV double resonance), whereas the K(+), Rb(+), and Cs(+) complexes exist in a single conformation. We analyze the structure of the conformers with the aid of density functional theory (DFT) calculations. In the Li(+) and Na(+) complexes, DB18C6 distorts the ether ring to fit the cavity size to the small diameter of Li(+) and Na(+). In the complexes with K(+), Rb(+), and Cs(+), DB18C6 adopts a boat-type (C(2v)) open conformation. The K(+) ion is captured in the cavity of the open conformer thanks to the optimum matching between the cavity size and the ion diameter. The Rb(+) and Cs(+) ions sit on top of the ether ring because they are too large to enter the cavity of the open conformer. According to time-dependent DFT calculations, complexes that are highly distorted to hold metal ions open the ether ring upon S(1)-S(0) excitation, and this is confirmed by extensive low-frequency progressions in the UVPD spectra.     

Monovalent ion adsorption at the muscovite (001)-solution interface: relationships among ion coverage and speciation, interfacial water structure, and substrate relaxation

The interfacial structure between the muscovite (001) surface and aqueous solutions containing monovalent cations (3 × 10(-3) m Li(+), Na(+), H(3)O(+), K(+), Rb(+), or Cs(+), or 3 × 10(-2) m Li(+) or Na(+)) was measured using in situ specular X-ray reflectivity. The element-specific distribution of Rb(+) was also obtained with resonant anomalous X-ray reflectivity. The results demonstrate complex interdependencies among adsorbed cation coverage and speciation, interfacial hydration structure, and muscovite surface relaxation. Electron-density profiles of the solution near the surface varied systematically and distinctly with each adsorbed cation. Observations include a broad profile for H(3)O(+), a more structured profile for Li(+) and Na(+), and increasing electron density near the surface because of the inner-sphere adsorption of K(+), Rb(+), and Cs(+) at 1.91 ± 0.12, 1.97 ± 0.01, and 2.26 ± 0.01 ?, respectively. Estimated inner-sphere coverages increased from ~0.6 to 0.78 ± 0.01 to ~0.9 per unit cell area with decreasing cation hydration strength for K(+), Rb(+), and Cs(+), respectively. Between 7 and 12% of the Rb(+) coverage occurred as an outer-sphere species. Systematic trends in the vertical displacement of the muscovite lattice were observed within ~40 ? of the surface. These include a <0.1 ? shift of the interlayer K(+) toward the interface that decays into the crystal and an expansion of the tetrahedral-octahedral-tetrahedral layers except for the top layer in contact with solution. The distortion of the top tetrahedral sheet depends on the adsorbed cation, ranging from an expansion (by ~0.05 ? vertically) in 3 × 10(-3)m H(3)O(+) to a contraction (by ~0.1 ?) in 3 × 10(-3) m Cs(+). The tetrahedral tilting angle in the top sheet increases by 1 to 4° in 3 × 10(-3) m Li(+) or Na(+), which is similar to that in deionized water where the adsorbed cation coverages are insufficient for full charge compensation.     

The solvent extraction of alkali metal picrates with 4,13-N,N'-dibenzyl-4,13-diaza-18-crown-6

Extraction of alkali metal picrates with N,N'-dibenzyl-18-crown-6 was carried out, with dichloromethane as water-immiscible solvent, as a function [ligand]/[metal cation]. The extractability of metal picrates (Li(+), Na(+), K(+), Rb(+), Cs(+)) was evaluated as a function of [L]/[M(+)]. The extractability of complex cation-picrate ion pairs decreases in this sequence: Li(+)>Rb(+)>Cs(+)>K(+)>Na(+). The overall extraction equilibrium constants (K(ex)) for complexes of N,N'-dibenzyl-18-crown-6 with alkali metal picrates between dichloromethane and water have been determined at 25 degrees C. The values of the extraction constants (logK(ex)) were determined to be 10.05, 6.83, 7.12, 7.83, 6.73 for Li(+), Na(+), K(+), Rb(+) and Cs(+) compounds, respectively. DB186 shows almost 2-fold extractability against Li(+) compared to the other metal picrates, whereas it shows no obvious extractability difference amongst the other metal cations when [L]/[M(+)] is 0.2-1. However, an increasing extractability is observed for Cs(+) when [L]/[M(+)] [1].     

A novel rearrangement in electrospray ionization multistage tandem mass spectrometry of amino acid ester cyclohexyl phosphoramidates of AZT

Several amino acid ester cyclohexyl phosphoramidates of AZT as anti-HIV prodrugs were synthesized and investigated by electrospray ionization tandem mass spectrometry (ESI-MS(n)). A novel methoxy group migration from the carbonyl group to the phosphoryl group was observed in ESI-MS2. This migration is believed to be a general pathway for ions with a methyl ester moiety at the gamma-position to a phosphoric acid moiety, which is assisted with metal ions such as Li(+), Na(+) and K(+). Coordination between metal ions with both the carbonyl oxygen and phosphoryl oxygen might be a key factor responsible for this migration.     

Competition between pi and non-pi cation-binding sites in aromatic amino acids: a theoretical study of alkali metal cation (Li+, Na+, K+)-phenylalanine complexes

To understand the cation-pi interaction in aromatic amino acids and peptides, the binding of M(+) (where M(+) = Li(+), Na(+), and K(+)) to phenylalanine (Phe) is studied at the best level of density functional theory reported so far. The different modes of M(+) binding show the same order of binding affinity (Li(+)>Na(+)>K(+)), in the approximate ratio of 2.2:1.5:1.0. The most stable binding mode is one in which the M(+) is stabilized by a tridentate interaction between the cation and the carbonyl oxygen (O[double bond]C), amino nitrogen (--NH(2)), and aromatic pi ring; the absolute Li(+), Na(+), and K(+) affinities are estimated theoretically to be 275, 201, and 141 kJ mol(-1), respectively. Factors affecting the relative stabilities of various M(+)-Phe binding modes and conformers have been identified, with ion-dipole interaction playing an important role. We found that the trend of pi and non-pi cation bonding distances (Na(+)-pi>Na(+)-N>Na(+)-O and K(+)-pi>K(+)-N>K(+)-O) in our theoretical Na(+)/K(+)-Phe structures are in agreement with the reported X-ray crystal structures of model synthetic receptors (sodium and potassium bound lariat ether complexes), even though the average alkali metal cation-pi distance found in the crystal structures is longer. This difference between the solid and the gas-phase structures can be reconciled by taking the higher coordination number of the cations in the lariat ether complexes into account.     

UV and IR spectroscopy of cold 1,2-dimethoxybenzene complexes with alkali metal ions

We report UV photodissociation (UVPD) and IR-UV double-resonance spectra of 1,2-dimethoxybenzene (DMB) complexes with alkali metal ions, M(+)·DMB (M = Li, Na, K, Rb, and Cs), in a cold, 22-pole ion trap. The UVPD spectrum of the Li(+) complex shows a strong origin band. For the K(+)·DMB, Rb(+)·DMB, and Cs(+)·DMB complexes, the origin band is very weak and low-frequency progressions are much more extensive than that of the Li(+) ion. In the case of the Na(+)·DMB complex, spectral features are similar to those of the K(+), Rb(+), and Cs(+) complexes, but vibronic bands are not resolved. Geometry optimization with density functional theory indicates that the metal ions are bonded to the oxygen atoms in all the M(+)·DMB complexes. For the Li(+) complex in the S(0) state, the Li(+) ion is located in the same plane as the benzene ring, while the Na(+), K(+), Rb(+), and Cs(+) ions are located off the plane. In the S(1) state, the Li(+) complex has a structure similar to that in the S(0) state, providing the strong origin band in the UV spectrum. In contrast, the other complexes show a large structural change in the out-of-plane direction upon S(1)-S(0) excitation, which results in the extensive low-frequency progressions in the UVPD spectra. For the Na(+)·DMB complex, fast charge transfer occurs from Na(+) to DMB after the UV excitation, making the bandwidth of the UVPD spectrum much broader than that of the other complexes and producing the photofragment DMB(+) ion.     

Study of ion specific interactions of alkali cations with dicarboxylate dianions

Alkali metal cations often show pronounced ion-specific interactions and selectivity with macromolecules in biological processes, colloids, and interfacial sciences, but a fundamental understanding about the underlying microscopic mechanism is still very limited. Here we report a direct probe of interactions between alkali metal cations (M(+)) and dicarboxylate dianions, (-)O(2)C(CH(2))(n)CO(2)(-) (D(n)(2-)) in the gas phase by combined photoelectron spectroscopy (PES) and ab initio electronic structure calculations on nine M(+)-D(n)(2-) complexes (M = Li, Na, K; n = 2, 4, 6). PES spectra show that the electron binding energy (EBE) decreases from Li(+) to Na(+) to K(+) for complexes of M(+)-D(2)(2-), whereas the order is Li(+) < Na(+) ≈ K(+) when M(+) interacts with a more flexible D(6)(2-) dianion. Theoretical modeling suggests that M(+) prefers to interact with both ends of the carboxylate -COO(-) groups by bending the flexible aliphatic backbone, and the local binding environments are found to depend upon backbone length n, carboxylate orientation, and the specific cation M(+). The observed variance of EBEs reflects how well each specific dicarboxylate dianion accommodates each M(+). This work demonstrates the delicate interplay among several factors (electrostatic interaction, size matching, and strain energy) that play critical roles in determining the structures and energetics of gaseous clusters as well as ion specificity and selectivity in solutions and biological systems.     

Oligoether-strapped calix[4]pyrrole: an ion-pair receptor displaying cation-dependent chloride anion transport

A ditopic ion-pair receptor (1), which has tunable cation- and anion-binding sites, has been synthesized and characterized. Spectroscopic analyses provide support for the conclusion that receptor 1 binds fluoride and chloride anions strongly and forms stable 1:1 complexes ([1·F](-) and [1·Cl](-)) with appropriately chosen salts of these anions in acetonitrile. When the anion complexes of 1 were treated with alkali metal ions (Li(+), Na(+), K(+), Cs(+), as their perchlorate salts), ion-dependent interactions were observed that were found to depend on both the choice of added cation and the initially complexed anion. In the case of [1·F](-), no appreciable interaction with the K(+) ion was seen. On the other hand, when this complex was treated with Li(+) or Na(+) ions, decomplexation of the bound fluoride anion was observed. In contrast to what was seen with Li(+), Na(+), K(+), treating [1·F](-) with Cs(+) ions gave rise to a stable, host-separated ion-pair complex, [F·1·Cs], which contains the Cs(+) ion bound in the cup-like portion of the calix[4]pyrrole. Different complexation behavior was seen in the case of the chloride complex, [1·Cl](-). Here, no appreciable interaction was observed with Na(+) or K(+). In contrast, treating with Li(+) produces a tight ion-pair complex, [1·Li·Cl], in which the cation is bound to the crown moiety. In analogy to what was seen for [1·F](-), treatment of [1·Cl](-) with Cs(+) ions gives rise to a host-separated ion-pair complex, [Cl·1·Cs], in which the cation is bound to the cup of the calix[4]pyrrole. As inferred from liposomal model membrane transport studies, system 1 can act as an effective carrier for several chloride anion salts of Group 1 cations, operating through both symport (chloride+cation co-transport) and antiport (nitrate-for-chloride exchange) mechanisms. This transport behavior stands in contrast to what is seen for simple octamethylcalix[4]pyrrole, which acts as an effective carrier for cesium chloride but does not operates through a nitrate-for-chloride anion exchange mechanism.     

Alkali-ion microsolvation with benzene molecules

The target of this investigation is to characterize by a recently developed methodology, the main features of the first solvation shells of alkaline ions in nonpolar environments due to aromatic rings, which is of crucial relevance to understand the selectivity of several biochemical phenomena. We employ an evolutionary algorithm to obtain putative global minima of clusters formed with alkali-ions (M(+)) solvated with n benzene (Bz) molecules, i.e., M(+)-(Bz)(n). The global intermolecular interaction has been decomposed in Bz-Bz and in M(+)-Bz contributions, using a potential model based on different decompositions of the molecular polarizability of benzene. Specifically, we have studied the microsolvation of Na(+), K(+), and Cs(+) with benzene molecules. Microsolvation clusters up to n = 21 benzene molecules are involved in this work and the achieved global minimum structures are reported and discussed in detail. We observe that the number of benzene molecules allocated in the first solvation shell increases with the size of the cation, showing three molecules for Na(+) and four for both K(+) and Cs(+). The structure of this solvation shell keeps approximately unchanged as more benzene molecules are added to the cluster, which is independent of the ion. Particularly stable structures, so-called "magic numbers", arise for various nuclearities of the three alkali-ions. Strong "magic numbers" appear at n = 2, 3, and 4 for Na(+), K(+), and Cs(+), respectively. In addition, another set of weaker "magic numbers" (three per alkali-ion) are reported for larger nuclearities.     

Structure of cationized arginine (arg.m, m = h, li, na, k, rb, and cs) in the gas phase: further evidence for zwitterionic arginine

The gas-phase structures of cationized arginine, Arg.M(+), M = Li, Na, K, Rb, and Cs, were studied both by hybrid method density functional theory calculations and experimentally using low-energy collisionally activated and thermal radiative dissociation. Calculations at the B3LYP/LACVP++** level of theory show that the salt-bridge structures in which the arginine is a zwitterion (protonated side chain, deprotonated C-terminus) become more stable than the charge-solvated structures with increasing metal ion size. The difference in energy between the most stable charge-solvated structure and salt-bridge structure of Arg.M(+) increases from -0.7 kcal/mol for Arg.Li(+) to +3.3 kcal/mol for Arg.Cs(+). The stabilities of the salt-bridge and charge-solvated structures reverse between M = Li and Na. These calculations are in good agreement with the results of dissociation experiments. The low-energy dissociation pathways depend on the cation size. Arginine complexed with small cations (Li and Na) loses H(2)O, while arginine complexed with larger cations (K, Rb, and Cs) loses NH(3). Loss of H(2)O must come from a charge-solvated ion, whereas the loss of NH(3) can come from the protonated side chain of a salt-bridge structure. The results of dissociation experiments using several cationized arginine derivatives are consistent with the existence of these two distinct structures. In particular, arginine methyl esters, which cannot form salt bridges, dissociate by loss of methanol, analogous to loss of H(2)O from Arg.M(+); no loss of NH(3) is observed. Although dissociation experiments probe gas-phase structure indirectly, the observed fragmentation pathways are in good agreement with the calculated lowest energy isomers. The combination of the results from experiment and theory provides strong evidence that the structure of arginine-alkali metal ion complexes in the gas phase changes from a charge-solvated structure to a salt-bridge structure as the size of the metal ion increases.     

Non-covalent interactions of alkali metal cations with singly charged tryptic peptides

The complexes formed by alkali metal cations (Cat(+) = Li(+), Na(+), K(+), Rb(+)) and singly charged tryptic peptides were investigated by combining results from the low-energy collision-induced dissociation (CID) and ion mobility experiments with molecular dynamics and density functional theory calculations. The structure and reactivity of [M + H + Cat](2+) tryptic peptides is greatly influenced by charge repulsion as well as the ability of the peptide to solvate charge points. Charge separation between fragment ions occurs upon dissociation, i.e. b ions tend to be alkali metal cationised while y ions are protonated, suggesting the location of the cation towards the peptide N-terminus. The low-energy dissociation channels were found to be strongly dependant on the cation size. Complexes containing smaller cations (Li(+) or Na(+)) dissociate predominantly by sequence-specific cleavages, whereas the main process for complexes containing larger cations (Rb(+)) is cation expulsion and formation of [M + H](+). The obtained structural data might suggest a relationship between the peptide primary structure and the nature of the cation coordination shell. Peptides with a significant number of side chain carbonyl oxygens provide good charge solvation without the need for involving peptide bond carbonyl groups and thus forming a tight globular structure. However, due to the lack of the conformational flexibility which would allow effective solvation of both charges (the cation and the proton) peptides with seven or less amino acids are unable to form sufficiently abundant [M + H + Cat](2+) ion. Finally, the fact that [M + H + Cat](2+) peptides dissociate similarly as [M + H](+) (via sequence-specific cleavages, however, with the additional formation of alkali metal cationised b ions) offers a way for generating the low-energy CID spectra of 'singly charged' tryptic peptides.     

Design and synthesis of luminescence chemosensors based on alkynyl phosphine gold(I)-copper(I) aggregates

Receptor-containing polynuclear mixed-metal complexes of gold(I)-copper(I) 1-3 based on a [{Au(3)Cu(2)(C≡CPh)(6)}Au(3){PPh(2)-C(6)H(4)-PPh(2)}(3)](2+) (Au(6)Cu(2)) core with benzo-15-crown-5, oligoether and urea binding sites were designed and synthesized, respectively. These complexes exhibited remarkably strong red emission at ca. 619-630 nm in dichloromethane solution at room temperature upon photoexcitation at λ > 400 nm, with the emission quantum yield in the range 0.59-0.85. The cation-binding properties of 1 and 2 and the anion-binding properties of 3 were studied using UV-vis, emission and (1)H NMR techniques. Complex 1, with six benzo-15-crown-5 pendants, was found to show a higher binding preference for K(+), with a selectivity trend of K(+)? Cs(+) > Na(+) > Li(+). The addition of metal ions (Li(+), Na(+), K(+) and Cs(+)) to complex 1 led to a modest emission enhancement with a concomitant slight blue shift in energy and well-defined isoemissive points, which is attributed to the rigidity of the structure and the inhibited PET (photo-induced electron transfer) process from the oxygen to the aggregate as a result of the binding of the metal ion. The six urea receptor groups on complex 3 were found to form multiple hydrogen bonding interactions with anions, with the positive charge providing additional electrostatic interaction for anion-binding. The anion selectivity of 3 follows the trend F(-) > Cl(-)≈ H(2)PO(4)(-) > Br(-) and the highest affinity towards F(-) is attributed to the stronger basicity of F(-), as well as its good size match with the cavity of the urea pocket.     

Encapsulation of metal cations by the PhePhe ligand: a cation-π ion cage

Structures and binding thermochemistry are investigated for protonated PhePhe and for complexes of PhePhe with the alkaline-earth ions Ba(2+) and Ca(2+), the alkali-metal ions Li(+), Na(+), K(+), and Cs(+), and the transition-metal ion Ag(+). The two neighboring aromatic side chains open the possibility of a novel encapsulation motif of the metal ion in a double cation-π configuration, which is found to be realized for the alkaline-earth complexes and, in a variant form, for the Ag(+) complex. Experimentally, complexes are formed by electrospray ionization, trapped in an FT-ICR mass spectrometer, and characterized by infrared multiple photon dissociation (IRMPD) spectroscopy using the free electron laser FELIX. Interpretation is assisted by thermochemical and IR spectral calculations using density functional theory (DFT). The IRMPD spectrum of protonated PhePhe is reproduced with good fidelity by the calculated spectrum of the most stable conformation, although the additional presence of the secondmost stable conformation is not excluded. All metal-ion complexes have charge-solvated binding modes, with zwitterion (salt bridge) forms being much less stable. The amide oxygen always coordinates to the metal ion, as well as at least one phenyl ring (cation-π interaction). At least one additional chelation site is always occupied, which may be either the amino nitrogen or the carboxy carbonyl oxygen. The alkaline-earth complexes prefer a highly compact caged structure with both phenyl rings providing cation-π stabilization in a "sandwich" configuration (OORR chelation). The alkali-metal complexes prefer open-cage structures with only one cation-π interaction, except perhaps Cs(+). The Ag(+) complex shows a unique preference for the closed-cage amino-bound NORR structure. Ligand-driven perturbations of normal-mode frequencies are generally found to correlate linearly with metal-ion binding energy.     

Dissection of the difference between the group I metal ions in inhibiting GSK3β: a computational study

Glycogen synthase kinase 3β (GSK3β) is a serine/threonine kinase that requires two cofactor Mg(2+) ions for catalysis in regulating many important cellular signals. Experimentally, Li(+) is a competitive inhibitor of GSK3β relative to Mg(2+), while this mechanism is not experienced with other group I metal ions. Herein, we use native Mg(2)(2+)-Mg(1)(2+) GSK3β and its Mg(2)(2+)-M(1)(+) (M = Li, Na, K, and Rb) derivatives to investigate the effect of metal ion substitution on the mechanism of inhibition through two-layer ONIOM-based quantum mechanics/molecular mechanics (QM/MM) calculations and molecular dynamics (MD) simulations. The results of ONIOM calculations elucidate that the interaction of Na(+), K(+), and Rb(+) with ATP is weaker compared to that of Mg(2+) and Li(+) with ATP, and the critical triphosphate moiety of ATP undergoes a large conformational change in the Na(+), K(+), and Rb(+) substituted systems. As a result, the three metal ions (Na(+), K(+), and Rb(+)) are not stable and depart from the active site, while Mg(2+) and Li(+) can stabilize in the active site, evident in MD simulations. Comparisons of Mg(2)(2+)-Mg(1)(2+) and Mg(2)(2+)-Li(1)(+) systems reveal that the inline phosphor-transfer of ATP and the two conserved hydrogen bonds between Lys85 and ATP, together with the electrostatic potential at the Li(1)(+) site, are disrupted in the Mg(2)(2+)-Li(1)(+) system. These computational results highlight the possible mechanism why Li(+) inhibits GSK3β.     

Isomer population analysis of gaseous ions from infrared multiple photon dissociation kinetics

Infrared multiple photon dissociation (IRMPD) kinetics measured with tunable laser radiation from a free electron laser (FEL) are used to probe the relative populations of and interconversions between energetically competitive isomers of gas-phase ions at 298 K. On-resonance IRMPD kinetics of monoisomeric benzoate anion and anilinium (protonated aniline) are measured to determine the extent of overlap of the laser beam with the precursor ion population (～93%). IRMPD kinetics indicating different photodissociation behavior for different isomers obtained at isomer-specific resonances are used to determine relative populations of salt bridge and charge-solvated isomers for ArgGly·Na(+), Ser·Cs(+), and Arg·Na(+). These values and Gibbs free energy differences obtained from them for thermal precursor populations are compared to values reported using other, less direct population probes. Rapid interconversion of two charge-solvated isomers occurs for ArgGly·Li(+), precluding population analysis for this ion. ArgGly·Na(+), ArgGly·Li(+), and Arg·Na(+) exhibit IRMPD induction periods lasting many seconds for some isomers at the laser photon energies and power used, indicating that IRMPD relative spectral intensities are time-dependent for these ions and that the relative band intensities in IRMPD spectra measured with short irradiation times may not provide meaningful information about relative isomer populations. These results constitute the first direct probe of ion isomer populations using IRMPD kinetics obtained with a FEL and illustrate a number of caveats in interpreting IRMPD spectra measured with just a single irradiation time. These results also indicate that more complete overlap of the laser beam with the ions will be highly advantageous in future instrument designs for IRMPD kinetics and spectroscopy experiments.     

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(+).     

A method for the determination of potentiometric selectivity coefficients of ion selective electrodes in the presence of several interfering ions

In this work a new method is reported for the determination of potentiometric selectivity coefficients of ion-selective electrode in which, similar to real samples, several interfering ions are simultaneously present in test solutions and where the electrode shows its practical behavior. In order to illustrate this method, the potentiometric selectivity coefficients of a commercial liquid membrane ammonium selective electrode is determined for biologically important interfering ions: Li(+), Na(+) and K(+).     

Solvent effects on the conformation of DNA dodecamer segment: a simulation study

Different solvent temperatures with five kinds of counterions are used to investigate solvent effects on the DNA microscopic structure. The dodecamer d (CGCGAATTCGCG) DNA segment is merged into the solvents and its conformation transition is studied with the molecular dynamics simulations in detail. For the simple point charge model of water molecule with Na(+) counterions, as temperature increases from 200 K to 343 K, the duplex DNA changes from stiff B form to a state between A form and B form, which we define as mixed (A-B) structure, with a double helix unwinding. To study the counterions effects, other four alkali cations, Li(+), K(+), Rb(+), or Cs(+) ions, are substituted for Na(+) ions at 298 K and 343 K, respectively. For the cases of Li(+), Rb(+), and Cs(+) ions, the duplex DNA becomes more flexible with sugar configuration changing form C2'-endo to C1'-endo type and the width and depth of minor groove at CpG and GpC steps moving towards A values, as the mass of the counterions decreasing. For the case of K(+) ions, DNA-K(+) interaction widens the width of minor and major grooves at ApA steps and TpT steps, respectively. It seems that the light ions (Li(+) or Na(+)) prefer to interact with the free phosphate oxygen atoms while the heavier ions (Rb(+) and Cs(+)) strongly interact with the base pairs.