Fragmentation of singly charged adenine induced by neutral fluorine beam impact at 3 keV

The fragmentation scheme of singly charged adenine molecule (H(5)C(5)N(5)(+)) has been studied via neutral fluorine impact at 3 keV. By analyzing in correlation the kinetic energy loss of the scattered projectile F(-) produced in single charge transfer process and the mass of the charged fragments, the excitation energy distribution of the parent adenine molecular ions has been determined for each of the main dissociation channels. Several fragmentation pathways unrevealed in standard mass spectra or in appearance energy measurements are investigated. Regarding the well-known hydrogen cyanide (HCN) loss sequence, we demonstrate that although the loss of a HCN is the dominant decay channel for the parent H(5)C(5)N(5)(+) (m = 135), the decay of the first daughter ion H(4)C(4)N(4)(+) (m = 108) involves not only the HNC (m = 27) loss but also the symmetric breakdown into two dimers of HCN.     

Structural properties of reciprocal form factor in neutral atoms and singly charged ions

Structural characteristics of the spherically averaged internally folded density or reciprocal form factor Br are studied within the Hartree-Fock framework for 103 neutral atoms, 54 singly charged cations, and 43 anions in their ground state. The function Br is classified throughout the Periodic Table into three types: (i) monotonic decrease from the origin, (ii) maximum at r=0 and a negative minimum at r>0, and (iii) a local maximum at r=0 and a pair maximum-minimum out of the origin. A detailed study of the corresponding properties for individual subshells as well as their relative weight for the total Br is also carried out. For completeness, the analytical Br for hydrogenlike atoms in both ground and excited states is also analyzed.     

Light-induced intermolecular proton transfer from gas-phase ions to neutral molecules

It is shown by use of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry that photoexcitation of protonated naphthalene by visible laser light of 488 nm can effect a proton transfer from this ion to acetonitrile. The reaction of the ground state reaction partners is endoergic by 31 kJ/mol.     

Dissociative excitation of the singly charged lead ion in electron collisions with PbCl2 molecules

Inelastic collisions of slow electrons with lead dichloride molecules yielding excited lead ions in a single encounter event were studied by the extended crossed-beam technique. At an incident electron energy of 100 eV, 67 cross sections for dissociative excitation of PbII spectral lines were measured. Three optical excitation functions were determined in the electron energy range 0–100 eV. The obtained results are compared with data on excitation cross sections of PbII in electron-atom collisions.     

Design of high-spin molecules incorporating charged plus neutral spin centers

A series of diradicals comprised of m-phenylene exchange coupling units and spin-bearing centers of the same (homo-spin) and different (hetero-spin) types were compared, using the semiempirical AM1-CI molecular orbital method. Two meta-coupled neutral (or charged) hetero-spin centers result in a high-spin ground state, while coupling of one neutral and one charged spin center gives rise to a low-spin ground state in the cases studied. The latter result is ascribed to the large splitting of partially occupied molecular orbitals by substitution, leading to dominance of purely ionic resonance structures in the singlet states of the monocharged “hetero-spin” cases. Effects of substitution and HOMO–LUMO splitting may be evaluated by computational methods to identify systems where resonance effects may override spin parity effects. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:161–167, 1998     

Electron-pair densities of singly charged atoms

For the singly charged 53 cations from Li⁺ to Cs⁺ and 43 anions from H⁻ to I⁻ in their ground states, spherically averaged electron-pair intracule (relative-motion) density h(u), extracule (center-of-mass-motion) density d(R), and their moments uⁿ and Rⁿ are examined, where u and R are the interelectronic distance and the center-of-mass radius of a pair of electrons, respectively. The intracule and extracule densities of all the 96 ions are found to be monotonically decreasing functions, as for neutral atoms. Approximate relations d(R)8h(2R) and uⁿ/Rⁿ2ⁿ are confirmed to be valid for the charged atoms as well.     

Application of a two-length-scale field theory to the solvation of neutral and charged molecules

We develop a continuous self-consistent theory of solute-water interactions that allows determination of the hydrophobic layer around a solute molecule of any geometry, with an explicit account of solvent structure described by its correlation function. We compute the mean solvent density profile n(r) surrounding the solute molecule as well as its solvation free energy deltaG. We compare the two-length-scale field theory to the numerical data of Monte Carlo simulations found in the literature for spherical molecules and discuss the possibility of self-consistent adjustment of the free parameters of the theory. In the framework of this approach, we compute the solvation free energies of alkane molecules and the free energy of interaction of two spheres of radius R separated by the distance D. We describe the general setting of the self-consistent account of electrostatic interactions in the framework of our model where the water is considered not as a continuous medium but as a gas of dipoles. We analyze the limiting cases where the proposed theory coincides with the electrostatics of a continuous medium.     

Separation of charged and neutral isotopic molecules by micellar electrokinetic chromatography in coated capillaries

Some unique separations are reported of pairs of deuterated and non-deuterated compounds by capillary zone electrophoresis (CZE) in coated capillaries in the absence and presence of surfactant micelles. Pyridine (pyridine-h₅) and [² H₅]pyridine (pyridine-d₅) could be separated in plain buffer (R = 1.1) and in 2% Nonidet P-40 (R = 1.5). Owing to the good separation obtained, it was possible to assess the degree of cross-contamination when “pure” isotopes were analysed. A 1:1 mixture of benzoic-h₅ and -d₅ acid was poorly separated in the absence of detergent (R = 0.39) but well separated in 50 mM sodium dodecyl sulphate (SDS) (R = 1.14). Benzyl-h₅ and -d₅ alcohol were reasonably well separated in a micellar system containing 50 mM SDS (R = 1.02) (a separation previously unreported in the literature. Benzene-h₆ and -d₆ were well separated again in presence of 50 mM SDS (R = 1.59). It appears that CZE offers a unique environment for the separation of positively and negatively charged and neutral isotope mixtures, previously reported only using RP-HPLC and GC.     

Activation analysis with charged particles

The principle and some applications of charged particle activation analysis are described. Important applications are the determination of light (B, C, N, O), medium (Ca, Fe) and heavy (Cd, Pb) elements in metals and semi-conductors and the analysis of geological and environmental materials.     

Activation analysis with charged particles

Sensitivity curves for detecting any element/isotope with Z = 20 to Z = 90, through 1, 2 and 3 particles emission reactions, activated with protons, deuterons and alphas of up to 35 MeV energy have been estimated and presented in graphical form. From these curves the detection sensitivity of any element/isotope in the aforementioned range, in any given matrix, can be directly obtained for an infinitely thick, a moderately thick or even a thin target. Furthermore, these curves would also help in selecting the most suitable nuclear reaction for the measurement of a particular element or isotope in a given matrix, and would also provide an indication of the unwanted and interfering activities being produced simultaneously.     

Activation analysis with charged particles

Activation methods are important because of their sensitivity. The accuracy and precision obtainable with charged-particle activation analysis (CPAA) have been significantly improved; the accuracy has been demonstrated in inter-laboratory and inter-method comparisons. The inherent complexity of CPAA makes it unsuitable for routine work, but the method is valuable for special applications, e.g., certification of reference materials, and for the determination of certain elements. Most applications concern the determination of light elements in metals and semi-conductor materials. After removal of surface layers by chemical etching, the concentrations of carbon, nitrogen and oxygen found by CPAA in some industrial metals, (e.g., aluminium, molybdenum and tungsten) proved to be orders of magnitude lower than expected from the results of other procedures. Other applications are the determination of medium- and high-Z elements, (e.g., calcium, cadmium, thallium and lead) in metals; these elements are very difficult to determine with neutron activation. Environmental powdered materials can be analyzed accurately; because of their low thermal conductivity, they must be irradiated under helium instead of vacuum to avoid volatilization of matrix components.     

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.     

Stability and spectroscopic properties of singly and doubly charged anions

Using density functional theory and hybrid B3LYP exchange-correlation energy functional we have studied the structure, stability, and spectroscopic properties of singly and doubly charged anions composed of simple metal atoms (Na, Mg, Al) decorated with halogens such as Cl and pseudohalogens such as CN. Since pseudohalogens mimic the chemistry of halogen atoms, our objective is to see if pseudohalogens can also form superhalogens much as halogens do and if the critical size for a doubly charged anion depends upon the ligand. The electron affinities of MCl(n) (M = Na, Mg, Al) exceed the value of Cl for n ≥ (k + 1), where k is the normal valence of the metal atom. However, for M(CN)(n) complexes this is only true when n = k + 1. In addition, while the electron affinities and vertical detachment energies of MCl(n) complexes are close to each other, they are markedly different when Cl is replaced by pseudohalogen, CN. The origin of these anomalous results is found to be due to the large binding energy of cyanogen, (NCCN) molecule. Because of the tendency of CN molecules to dimerize, the ground state geometries of the neutral and anionic M(CN)(n) complexes are very different when their number exceed the normal valence of the metal atom. While our calculations support the conclusion of Skurski and co-workers that pseudohalogens can form the building blocks of superhalogens, we show that there is a limitation on the number of CN moieties where this is true. Equally important, we find large differences between the ground state geometries of the neutral and anionic M(CN)(n) complexes for n ≥ (k + 2) which could play an important role in interpreting future experimental data on M(CN)(n) complexes. This is because the electron affinity defined as the energy difference between the ground states of the anion and neutral can be very different from the adiabatic detachment energy defined as the energy difference between the ground state of the anion and its structurally similar neutral isomer.     

Buffer system for the separation of neutral and charged small molecules using micellar electrokinetic chromatography with mass spectrometric detection

An organic buffer system will be discussed that is suitable for the separation of neutral as well as charged molecules be means of micellar electrokinetic chromatography (MEKC). The buffers are based on the combination of a long chain alkyl acid, such as lauric acid with ammonium hydroxide or an organic base such as tris-hydroxymethylaminomethane (Tris). The resulting buffer system is able to separate neutral compounds based on its micellar properties. These buffers exhibit much reduced conductivity compared to traditional MEKC buffers, such as sodium dodecylsulfate (SDS), which contain inorganic salts. They also have inherent buffer capacity at high pH resulting from the basic buffer component, which in our studies had pK values from about 8-11. The separations that were observed showed high efficiency with plate counts in many cases above 500,000 plates per meter. The reduced conductivity allowed for the application of much higher electric fields, resulting in very fast analysis times. Alternatively, an increase in detection sensitivity could be achieved, as the reduced conductivity allowed for the use of capillaries with lager internal diameters. Combinations of different alkyl acids and organic bases provided for significant flexibility in selectivity tuning. Finally, the fact that the organic micellar buffer systems discussed here do not contain inorganic ions, allows for coupling with mass spectrometric (MS) detection. The possibility of MS detection combined with the high speed in analysis that can be obtained using these organic buffer systems, could make this approach an interesting option for high throughput analysis of combinatorial libraries.     

Reactions of neutral gas-phase yttrium atoms with two cyclohexadiene isomers

The reactions of neutral ground-state yttrium (Y) atoms with 1,3- and 1,4-cyclohexadiene (CHD) were studied using crossed molecular beams. Formation of YC(6)H(6) + H(2) and YH(2) + C(6)H(6) was observed for both isomers at collision energies (E(coll)) of 31.3 and 13.0 kcal/mol. Measured product branching ratios at E(coll) = 31.3 kcal/mol indicated that YH(2) + C(6)H(6) was the dominant channel, accounting for >97% of the products. An additional minor product channel, YC(4)H(4) + C(2)H(4), was observed for 1,3-CHD at the higher E(coll). The reaction threshold for YC(4)H(4) formation was determined to be 29.5 ± 2.0 kcal/mol based on fits to the data.     

Acidity of adenine and adenine derivatives and biological implications. A computational and experimental gas-phase study

The gas-phase acidities of adenine, 9-ethyladenine, and 3-methyladenine have been investigated for the first time, using computational and experimental methods to provide an understanding of the intrinsic reactivity of adenine. Adenine is found to have two acidic sites, with the N9 site being 19 kcal mol(-1) more acidic than the N10 site; the bracketed acidities are 333 +/- 2 and 352 +/- 4 kcal mol(-1), respectively. Because measurement of the less acidic site can be problematic, we benchmarked the adenine N10 measurement by bracketing the acidity of 9-ethyladenine, which has the N9 site blocked and allows for exclusive measurement of the N10 site. The acidity of 9-ethyladenine brackets to 352 +/- 4 kcal mol(-1), comparable to that of the N10 site of the parent adenine. Calculations and experiments with 3-methyladenine, a harmful mutagenic nucleobase, uncovered the surprising result that the most commonly written tautomer of 3-methyladenine is not the most stable in the gas phase. We have found that the most stable tautomer is the "N10 tautomer" 10, as opposed to the imine tautomer 3. The bracketed acidity of 10 is 347 +/- 4 kcal mol(-1). Since 10 is not a viable species in DNA, 3 is a likely tautomer; calculations indicate that this form has an extremely high acidity (320-323 kcal mol(-1)). The biological implications of these results, particularly with respect to enzymes that cleave alkylated bases from DNA, are discussed.     

Interactions between charged surfaces with ionizable sites

A key factor controlling the interactions between surfaces in aqueous solutions is the surface charge density. Surfaces typically become charged though a titration process where surface groups can become ionized based on their dissociation constant and the pH of the solution. In this work, we use a Monte Carlo method to treat this process in a system with two planar surfaces with explicitly described ionizable sites in a salt solution. We focus on a system with a surface density of ionizable sites set to 4.8 nm(-2), corresponding to silica. We find that the surface charge density changes as the surfaces come close to contact due to interactions between the ionizable groups on each surface. In addition, we observe an attraction between the surfaces above a threshold surface charge, in good agreement with previous theoretical predictions based on uniformly charged surfaces. However, close to contact we find the force is significantly different than for the uniformly charged case.     

Analytical Hartree-Fock electron densities for singly charged cations and anions

The Hartree-Fock (HF) electron density has an important property that it is identical to the unknown exact density to the first order in the perturbation theory. We generate the spherically averaged HF electron density ρ(r) by using the numerical HF method for the singly charged 53 cations from Li⁺ to Cs⁺ and 43 anions from H⁻ to I⁻ in their ground state. The resultant density is then accurately fitted into an analytical function F(r), which is expressed by a linear combination of basis functions r ⁿⁱ exp(−ζ _i r). The present analytical approximation F(r) has the following properties: (1) F(r) is nonnegative, (2) F(r) is normalized, (3) F(r) reproduces the HF moments <r ^k > (k=−2 to +6), (4) F(0) is equal to ρ(0), (5) F ^′(0) satisfies the cusp condition and (6) F(r) has the correct exponential decay in the long-range asymptotic region. The present results together with our previous ones for neutral atoms provide a compilation of accurate analytical approximations of the HF electron densities for all the neutral and singly charged atoms with the number of electrons N≤54. Received: 11 July 1997 / Accepted: 27 August 1997     

Kronecker-product periodic systems of small gas-phase molecules and the search for order in atomic ensembles of any phase

The periodic law, manifested in the chart of the elements, is so fundamental in chemistry and related areas of physics that the question arises "Might periodicity among molecules also be embodied in a periodic system?" This review paper details how a particular periodic system of gas-phase diatomic molecules, allowing for the forecasting of thousands of new data, was developed. It can include ionized and even quarked-nuclei molecules and it coincides with locality (averaging) and the additivity found in some data; it has interesting vector properties, and it may be related in challenging ways to partial order. The review then explains how periodic systems for triatomic and four-atomic species are evolving along a similar path. The systems rest largely upon exhaustive comparisons of tabulated data, relate to some extent to the octet rule, and include reducible representations of the dynamic group SO(4) in higher spaces. Finally, the paper shows how periodicity can be quantified in data for larger molecules. Data for properties of homologous or substituted molecules, in any phase, are quantified with a vector index, and the index for one set can be transformed into that for another set.