Atomic Cations Research Articles

Gas-phase organic reactions of the atomic oxygen radical cation

Reactivity of ground-state oxygen radical cation, O+(4S), has been studied with several organic compounds for the first time. Rate constants and product distributions have been measured for the ion-neutral reactions of O+ with acetaldehyde, acetic acid, acetone, dimethyl ether, methanol, and methyl formate at 300K in a flowing-afterglow-selected ion flow tube (FA-SIFT). The reactions observed proceed efficiently, occurring above 50% of the collision rate in each case. We observed highly exothermic charge transfer reactions which lead to dissociation in some cases. Other interesting trends in reactivity include attack on methyl groups, and for some reactions, O+ replaces the methyl radical.

First-Principles Investigation on Structural and Optical Properties of M+@C60 (Where M = H, Li, Na, and K)

Structural and optical properties of proton and alkali-metal atom cation encapsulated inside C60 molecule, M+@C60 (where M = H, Li, Na, and K), are investigated in detail by first-principles. Two possible ground state atomic geometries where M+ can exist outside or inside C60 are proposed by the optimization using the B3LYP hybrid functional based on the density functional theory. From the potential energy surface obtained in the same level calculation, we confirm that the energy barrier existing at the surface of C60 plays an important role to confine M+ inside. We also apply an all-electron GW + Bethe–Salpeter method based on the many-body perturbation theory and calculate the (inverse) photoemission spectra and the photoabsorption spectra. The calculated spectra are in reasonable agreement with available experimental results, while minor deviation exists, suggesting a non-negligible environment effect.

Bond‐Forming Reactions of Small Triply Charged Cations with Neutral Molecules

Time-of-flight mass spectrometry reveals that atomic and small molecular triply charged cations exhibit extensive bond-forming chemistry, following gas-phase collisions with neutral molecules. These experiments show that at collision energies of a few eV, I(3+) reacts with a variety of small molecules to generate molecular monocations and molecular dications containing iodine. Xe(3+) and CS2(3+) react in a similar manner to I(3+), undergoing bond-forming reactions with neutrals. A simple model, involving relative product energetics and electrostatic interaction potentials, is used to account for the observed reactivity.

Density functional and tight binding theories of electronic properties of II–VI heterostructures

We present comparative calculations of the electronic structure of Cd and Zn based group II–VI compounds and their heterostructures based on the density functional and tight binding theories. The first principles density functional theory (DFT) uses the modified Becke–Johnson exchange potential with LDA correlation potential (MBJLDA) and the semi-empirical tight binding theory uses the first nearest neighbor (NN) sp3d5 and second nearest neighbor (2NN) sp3s⁎ basis with spin–orbit coupling of II cation (Cd, Zn) and VI anion (S, Se, Te) atoms for calculating the electronic structure of Cd and Zn based II–VI compounds and their heterostructures. The results of DFT with MBJLDA functional and NN sp3d5 and 2NN sp3s⁎ TB models are found to be in excellent agreement with measured band gaps of CdX and ZnX (X=S, Se, Te) based group II–VI compounds and their CdZnS/CdS, CdSTe/CdTe and ZnSSe/ZnSe heterostructures. We conclude that the NN sp3d5 TB model gives much more physical insight than the (2NN) sp3s⁎ TB model, making use of the fictitious s* state unnecessary.

Bromidobis[2-(pyridin-2-yl)methanol-κ2N,O]copper(II) bromide monohydrate

The title compound, [CuBr(C6H7NO)2]Br·H2O, is an ionic mononuclear complex in which the [CuBr(C6H7NO)2](+) cation possesses distorted square-pyramidal geometry. The Cu(II) centre is coordinated by two neutral 2-(pyridin-2-yl)methanol (2-pyMeOH) ligands and a terminal bromide ligand. The 2-pyMeOH ligands are coordinated in a bidentate chelating manner through the pyridine N and hydroxy O atoms, forming a five-membered chelate ring with the Cu(II) centre. The planes of the pyridine rings are twisted by 58.71 (14)° with respect to each other. The charge is balanced by a noncoordinating bromide anion which, together with a solvent water molecule, links the components through hydrogen bonds into infinite chains propagating along the a axis. The mononuclear cations appear to associate in pairs through weak interactions between the metal atom of one cation and the halogen atom of an adjacent cation.

Pyridinium bis(pyridine-κN)tetrakis(thiocyanato-κN)ferrate(III)

In the title compound, (C5H6N)[Fe(NCS)4(C5H5N)2], the FeIII ion is coordinated by four thio­cyanate N atoms and two pyridine N atoms in a trans arrangement, forming an FeN6 polyhedron with a slightly distorted octa­hedral geometry. Charge balance is achieved by one pyridinium cation bound to the complex anion via N—H⋯S hydrogen bonding. The asymmetric unit consists of one FeIII cation, four thio­cyanate anions, two coordinated pyridine mol­ecules and one pyridinium cation. The structure exhibits π–π inter­actions between pyridine rings [centroid–centroid distances = 3.7267 (2), 3.7811 (2) and 3.8924 (2) Å]. The N atom and a neighboring C atom of the pyridinium cation are statistically disordered with an occupancy ratio of 0.58 (2):0.42 (2).

Improper ferroelectricity and multiferroism in 2H-BaMnO3

Using first-principles calculations, we study theoretically the stable 2H hexagonal structure of BaMnO3. We show that from the stable high temperature P63/mmc structure, the compound should exhibit an improper ferroelectric structural phase transition to a P63cm ground state. Combined with its antiferromagnetic properties, 2H-BaMnO3 is therefore expected to be multiferroic at low temperature. The phase transition mechanism in BaMnO3 appears similar to what was reported in YMnO3 in spite of totally different atomic arrangement, cation sizes and Mn valence state.

Hydrogen-Bonding and the Dissolution Mechanism of Uracil in an Acetate Ionic Liquid: New Insights from NMR Spectroscopy and Quantum Chemical Calculations

The dissolution of uracil-a pyrimidine nucleic acid base-in the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][CH3COO]) has been investigated by methods of (1)H and (13)C NMR spectroscopy, (1)H-(1)H NOESY NMR spectroscopy, and quantum chemical calculations. The uracil-[C2mim][CH3COO] interactions that define the dissolution mechanism comprise the hydrogen bonds between the oxygen atoms of the acetate anion and the hydrogen atoms of the N1-H and N3-H groups of uracil and also the hydrogen bonds between the most acidic aromatic hydrogen atom (H2) of the imidazolium cation and the oxygen atoms of the carbonyl groups of uracil. The bifunctional solvation nature of the ionic liquid can be inferred from the presence of interactions between both ions of the ionic liquid and the uracil molecule. The location of such interaction sites was revealed using NMR data ((1)H and (13)C chemical shifts both in the IL and in the uracil molecule), complemented by DFT calculations. NOESY experiments provided additional evidence concerning the cation-uracil interactions.

Cis,cis,cis-(Acetato-κ2O,O′)bis[1,2-bis(diphenylphosphanyl)ethane-κ2P,P′]ruthenium(II) 0.75-trifluoromethanesulfonate 0.25-chloride

In the title RuII carboxyl­ate compound, [Ru(C2H3O2)(C26H24P2)2](CF3O3S)0.75Cl0.25, the distorted tris-bidentate octa­hedral stereochemistry about the RuII atom in the complex cation comprises four P-atom donors from two 1,2-bis­(diphenyl­phosphan­yl)ethane ligands [Ru—P = 2.2881 (13)–2.3791 (13) Å] and two O-atom donors from the acetate ligand [Ru—O = 2.191 (3) and 2.202 (3) Å]. The disordered counter-anions are located on the same site in the structure in a 3:1 ratio, the expanded formula comprising four complex cations, three trifluoro­methane­sulfonate anions and one chloride anion, with two such formula units in the unit cell.

Bromido(1,4,7,10,13-pentaazacyclohexadecane)cobalt(III) dibromide dihydrate

The title salt, [CoBr(C11H27N5)]Br2·2H2O, contains a complex cation with mirror symmetry and two Br− counter-anions that are likewise located on the mirror plane. The central CoIII atom of the complex cation has one Br− ion in an axial position, one N atom of the penta­dentate macrocyclic ligand in the other axial position and four N atoms of the ligand in equatorial positions, defining a distorted octa­hedral coordination geometry. The macrocyclic ligand is coordinated to the CoIII atom within a 5, 6, 5 arrangement of chelate rings in the equatorial plane of the four N atoms. Due to symmetry, the configuration of the chiral N atoms is 1RS, 4SR, 10RS, 13SR. In the crystal, N—H⋯Br, O—H⋯Br and N—H⋯O hydrogen bonds between the complex cation, anions and lattice water mol­ecules generate a three-dimensional network.

Evidence for Rod‐Shaped DNA‐Stabilized Silver Nanocluster Emitters

Fluorescent DNA-stabilized silver nanoclusters contain both cationic and neutral silver atoms. The absorbance spectra of compositionally pure solutions follow the trend expected for rod-shaped silver clusters, consistent with the polarized emission measured from individual nanoclusters. The data suggest a rod-like assembly of silver atoms, with silver cations mediating attachment to the bases.

3,5-Diphenyl-1,2,4-dithiazolium tetrabromidoferrate(III)

The cation of the title salt, (C14H10NS2)[FeBr4], contains a flat central NC2S2 ring (r.m.s. deviation = 0.005 Å), with two attached phenyl rings that are almost coplanar [the dihedral angles between the mean planes are 2.4 (1) and 7.7 (1)° for the two phenyl rings]. The [FeBr4]− anion makes short Br⋯S contacts [Br⋯S = 3.4819 (8), 3.6327 (9) and 3.5925 (9) Å] and also bridges by way of short contacts to ring H atoms of a second cation held parallel to the first by π-stacking, with a separation between the mean 1,2,4-dithia­zolium rings of 3.409 Å. The closest contacts are between a phenyl ring centroid of one cation and the ipso C atom of the phenyl ring of another cation, for which the distance is 3.489 Å. The discrete dimers are linked laterally by further Br⋯H short contacts, resulting in double sheets located parallel to the b axis and to the bis­ector of a and c.

Molecular motion in pyridazinium/crown ether supramolecular cation salts of a nickel dithiolene complex

Supramolecular cations formed by monoprotonated pyridazinium cations and cis-anti-cis-dicyclohexano[18]-crown-6 (DCH[18]-crown-6) or dibenzo[18]-crown-6 (DB[18]-crown-6) were introduced into [Ni(dmit)2]− salts (where dmit2− = 2-thione-1,3-dithiole-4,5-dithiolate). X-ray crystal structure analysis of (pyridazinium+)(DCH[18]-crown-6)[Ni(dmit)2]− (1) revealed a chair-type conformation of the DCH[18]-crown-6 moiety. A V-shaped conformation of the DB[18]-crown-6 moiety was observed in (pyridazinium+)(DB[18]-crown-6)2[Ni(dmit)2]−(H2O)2 (2). Nitrogen atoms in the pyridazinium cations interacted with the oxygen atoms of the DCH[18]-crown-6 and DB[18]-crown-6 through N–H+O hydrogen bonds, forming 1:1 and 1:2 supramolecular structures, respectively. Sufficient space for molecular motions of the pyridazinium cations, namely flip-flop and in-plane rotations, exists in salt 1. Disorder in nitrogen atoms was observed by X-ray analysis, indicating dynamic motion of the pyridazinium cation, namely flip-flop motion and in-plane motion. A potential energy calculation further supported the possibility of dynamic motion of cations in the crystal. By contrast, the flip-flop motion of the pyridazinium group in salt 2 is restricted by the two nearest-neighbouring DB[18]-crown-6 molecules. Weak antiferromagnetic intermolecular interactions between the [Ni(dmit)2]− anions in the two-dimensional layers of salt 1 were observed, resulting in alternating antiferromagnetic Heisenberg chain-type magnetic susceptibility. Quasi-one-dimensional intermolecular interactions between the [Ni(dmit)2]− anions were observed in salt 2, whose magnetic behaviour followed the Bonner–Fisher model.

A Quantum Monte Carlo Study of Lanthanum

Pseudopotential calculations of the ground state energies of the Lanthanum neutral atom, first and second corresponding cations by means of the variational Monte Carlo (VMC) and the diffusion Monte Carlo (DMC) methods are performed. The first and the second ionization potentials have been calculated for Lanthanum. The obtained results are satisfactory and comparable with the available experimental data. Studying the DMC energy of the La atom at different time steps, gave us a time step error of the order 0.0019 Hartree for the smallest time step, τ = 0.0001 Hartree-1, and -0.0104 Hartree for the largest time step, τ = 0.01 Hartree-1. This paper demonstrates the ability of extending the QMC method for lanthanides and obtaining highly accurate results.

Factors affecting the magnetic coupling in Sr2V3O9 type oxides: As for V substitution in the VO4 tetrahedra and nature of the cation

A density functional theory study of the magnetic couplings in Sr2V3O9 type magnetic oxides suggests that whereas the intrachain coupling is always weakly ferromagnetic, the interchain coupling may be antiferromagnetic or even weakly ferromagnetic depending on the nature of the central tetrahedral atom (As/V) cations, and, to a lesser extent, structural details.

55 Dynamics of the nucleosome core particle revealed from a new database of high resolution X-ray crystallographic and simulated structures

The nucleosome core particle is a highly conserved structure which can play diverse roles depending on the organism, cell, or part of chromatin in which it resides. The Protein Data Bank currently contains approximately 70 nucleosome core particle structures, over half of which were determined in the last three years. The recent emergence of the field of epigenetics, and the increase in data available from experiments, warrants a need to develop new approaches to quantitatively compare various features of interest across multiple structures. As a first step, we have developed a database and new computational tools to allow researchers to quantitatively analyze and compare the nucleosome core particle structures deposited in the Protein Data Bank. The features of the DNA-protein assembly can be examined in novel coordinate frames placed on the structure, allowing researchers to obtain a better understanding of the organization and subtleties of the macomolecular complexes. This comparison allows one to examine the ‘motion’ of any specific residue of interest, including sites of post-translational histone modification. The database also includes DNA-histone contact points, DNA conformational parameters, and information about protein features, such as the secondary structure in the globular histone core and the ‘motion’ of the histone tails. Along with these features, we also characterize the dynamics of the global structure of the nucleosome core particle, including the changes in superhelical path of the DNA and the rearrangements of the histone tetramers. In addition to data obtained from crystallographically solved structures, we are working to incorporate data from in silico experiments. The data and the results of the analysis are available to the public as an automatically updated, online-accessible web server. Cartoon diagrams of crystal structures are shown with their reference frames aligned. The frames were computed by PCA of the globular core of the histone octamer. The anionic atoms of aspartic acid and glutamic acid are marked in light red. The cationic atoms of the arginines and lysines are marked in dark blue. Note the channels that the charges may occupy.

Computational Studies of Ion Pairing. 7. Ion-Pairing and Association Effects between Tetraalkylammonium Ions and Nitrobenzene Redox Species. “Ion Pairing” to Neutral Substances

The structures of few ion pairs are known with any degree of certainty. In this work, the structures and energies of attraction in acetonitrile of nitrobenzene and its anion radical and dianion with a series of tetraalkylammonium ions of increasing size were computed by density functional theory. The resulting associated molecular pairs all exhibit the same unusual but chemically reasonable structure resulting from attraction between hydrogen atoms of the ammonium cation and the oxygen atoms of the nitro group. The cations form weak complexes with neutral nitrobenzene, stronger ion pairs with the monoanion, and strongly bound ion pairs with the dianion. The results delineate subtle issues governing the formation of such complexes that are directly relevant to issues of molecular recognition, self-assembly, and supramolecular chemistry.

Supramolecular diaryliodonium salt‐crown ether complexes as cationic photoinitiators

AbstractDiaryliodonium salts spontaneously form crystalline 1:1 supramolecular complexes at room temperature in good to excellent yields with 18‐crown‐6 ether and its cyclohexano‐ and benzo‐substituted analogs. The complexes were characterized using IR, UV, MS, 1H, and 13C‐NMR spectroscopy and by single crystal X‐ray crystallography. The analytical data obtained were consistent with a structure in which the positively charged iodine atom of diaryliodonium cation is positioned above and over the center of the crown ether ring with the positively charged iodine atom coordinated to the crown ether oxygen atoms. The diaryliodonium salt‐crown ether complexes are photosensitive and were used to carry out the photoinitiated cationic polymerizations of a number of mono‐ and difunctional monomers. During irradiation with UV light, the supramolecular complexes undergo photolysis with the generation of a Brønsted acid and with the concomitant release of the crown ether. When used as photoinitiators, the crown ether that is released markedly influences the kinetics of the subsequent cationic polymerization of the monomer. Further studies demonstrated that the photolysis of diaryliodonium salt‐crown ether supramolecular complexes can be photosensitized using typical‐electron transfer photosensitizers. Free radical‐promoted photosensitization using typical unimolecular free radical photoinitiators such as 2,2‐dimethoxy‐2‐phenylacetophenone also takes place readily. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013

Mechanism for the reactions of sulfides and sulfoxides with hypochlorites: racemization and oxygen exchange of oxysulfonium salts and sulfoxides

Density functional theory computations have been performed on the oxidations of sulfides and sulfoxides with hypochlorite ion (OCl−), hypochlorous acid, and alkyl hypochlorites to study the mechanism of the reactions. The OCl− anion transforms sulfides to sulfoxides and sulfoxides to sulfones in oxygen transfers. The oxygen atom of QOCl hypochlorites (Q = H, Me, t‐Bu) attacks at the sulfur atom of the substrates, and oxysulfonium cation intermediates are formed; the departure of the leaving Cl− is catalyzed by soft Lewis acids. The structures of the early transition states are determined by highest occupied molecular orbital–lowest unoccupied molecular orbital interactions. The sulfur compounds are the electron acceptors in the reaction with OCl−, but they are the electron donors in the reactions with QOCl. The attack of Cl− at the oxygen atom of oxysulfonium cation intermediates leads to the sulfide and QOCl precursors and can result in racemization, oxygen exchange, and reduction of oxysulfonium salts in reversible reactions. The attack of Cl− at the sulfur atom of oxysulfonium salts produces λ4‐sulfane intermediates. Oxysulfonium cations can be transformed into sulfoxide products with the attack of Cl− or water at the α‐carbon atom of the O‐alkyl group. The attack of water at the sulfur atom of oxysulfonium cation leads to hydrolysis or oxygen exchange reactions. Racemization and oxygen exchange of sulfoxides proceeds in similar reactions, through the formation of hydroxysulfonium cation intermediates in acidic media in the presence of Cl−. Chlorosulfonium cations are of very high energy; their intermediacy can be ruled out in the reactions of sulfides with hypochlorites. Copyright © 2012 John Wiley & Sons, Ltd.

The Equilibrium Structure of Lithium Salt Solutions in Ether-Functionalized Ammonium Ionic Liquids

Molecular dynamics simulations have been performed for ionic liquids based on a ternary mixture of lithium and ammonium cations and a common anion, bis(trifluoromethylsulfonyl)imide, [Tf(2)N](-). We address structural changes resulting from adding Li(+) in ionic liquids with increasing length of an ether-functionalized chain in the ammonium cation. The calculation of static structure factors reveals the lithium effect on charge ordering and intermediate range order in comparison with the neat ionic liquids. The charge ordering is modified in the lithium solution because the coordination of [Tf(2)N](-) toward Li(+) is much stronger than ammonium cations. Intermediate range order is observed in neat ionic liquids based on ammonium cations with a long chain, but in the lithium solutions, there is also a nonhomogenous distribution of Li(+) cations. The presence of Li(+) enhances interactions between the ammonium cations due to correlations between the oxygen atom of the ether chain and the nitrogen atom of another ammonium cation.