Ions In Molecules Research Articles

Fabrication of gold clusters photoreduced in gold-dendrimer complex nanoparticles

Au clusters, embedded in a dendrimer nanoparticle, have been successfully fabricated by photoreduction of gold ion-dendrimer complex nanoparticles that were fabricated using the reprecipitation method. The electron microscope observations suggested that the Au cluster was formed in an individual gold ion-dendrimer complex after 10 min of UV irradiation. As a result, Au clusters with 1.3 ± 0.6 nm were obtained as a minimum size. In addition, the final size of Au clusters can be controlled by changing UV irradiation time through the aggregation (or fusion) of Au clusters and/or Au ions in several dendrimer molecules.

Structure/ Dielectric properties relationships in nematic liquid crystal cells/ Calixarene alignment layers interactions

The dielectric relaxation of a nematic liquid crystal (NLC) cells, induced by several calixarene layers, has been investigated. The alignment layers were deposited onto the ITO slides using an evaporation technique and categorized using wettability technique and atomic force microscopy (AFM). These treated plates were used to prepare liquid crystal cells which induce a planar orientation of the NLC molecules. It has been shown that the calixarene alignment layers have a blocking effect on the liquid crystal cell at a high frequency. It has also been established that the dielectric relaxation is caused by the double layer formed by the adsorption of impurity ions in (NLC) molecules onto the electrode surfaces of the cells. The dielectric behavior of nematic liquid crystal cells was studied by impedance spectroscopy in frequency range, from 1mHz to 13MHz. The Nyquist diagrams are discussed in term of equivalent electrical circuit.

Electrochemical treatment of poorly biodegradable DPC cationic surfactant

The electrochemical oxidation of the cationic surfactant dodecylpyridinium chloride (DPC) was investigated using an electrolytic flow cell operating in batch recycle mode under galvanostatic conditions. The cell was equipped with a boron-doped diamond anode and a stainless steel cathode. The effects of some operating parameters, such as current density, recirculation flow-rate, and DPC concentration were investigated. DPC removal and mineralization were monitored by HPLC analyses and TOC measurements. The results show that DPC can be successfully removed and that degradation is under mass-transport control. The oxidation rate was well described by pseudo-first-order kinetics, and while the apparent rate constant increased with flow-rate, it was unaffected by DPC concentration and current density. Under optimum 5mAcm−2 and 300dm3h−1 conditions, the apparent rate constant was 3.13×10−4s−1. DPC solution with 75mgdm−3 of surfactant (54mgdm−3 of initial TOC) was completely mineralized in 330min, achieving maximum 33% efficiency. Anodic oxidation of the cationic DPC was compared with anionic sodium dodecyl benzene sulfonate (SDBS) degradation and DPC oxidation was demonstrated to be faster and requiring less energy due to the presence of chloride ions in the DPC molecules that are oxidized to active chlorine which acts as redox mediator increasing the removal rate.

Revealing the consequences and errors of substance arising from the inverse confusion between the crystal (ligand) field quantities and the zero-field splitting ones

Survey of recent literature has revealed a doubly-worrying tendency concerning the treatment of the two distinct types of Hamiltonians, namely, the physical crystal field (CF), or equivalently ligand field (LF), Hamiltonians and the zero-field splitting (ZFS) Hamiltonians, which appear in the effective spin Hamiltonians (SH). The nature and properties of the CF (LF) Hamiltonians have been mixed up in various ways with those of the ZFS Hamiltonians. Such cases have been identified in a rapidly growing number of studies of the transition-ion based systems using electron magnetic resonance (EMR), optical spectroscopy, and magnetic measurements. These findings have far ranging implications since these Hamiltonians are cornerstones for interpretation of magnetic and spectroscopic properties of the single transition ions in various crystals or molecules as well as the exchange coupled systems (ECS) of transition ions, e.g. single molecule magnets (SMM) or single ion magnets (SIM). The seriousness of the consequences of such conceptual problems and related terminological confusions has reached a level that goes far beyond simple semantic issues or misleading keyword classifications of papers in journals and scientific databases. The prevailing confusion, denoted as the CF=ZFS confusion, pertains to the cases of labeling the true ZFS quantities as purportedly the CF (LF) quantities. Here we consider the inverse confusion between the CF (LF) quantities and the SH (ZFS) ones, denoted the ZFS=CF confusion, which consists in referring to the parameters (or Hamiltonians), which are the true CF (LF) quantities, as purportedly the ZFS (or SH) quantities. Specific cases of the ZFS=CF confusion identified in recent textbooks, reviews and papers, especially SMM- and SIM-related ones, are surveyed and the pertinent misconceptions are clarified. The serious consequences of the terminological confusions include misinterpretation of data from a wide range of experimental techniques and, most recently, have lead to pitfalls and errors of substance bearing on understanding of physical properties. Clarification of the incorrect terminology is timely in order to bring about better understanding of the physical principles and prevent further proliferation of the confusion.

Terminological confusions and problems at the interface between the crystal field Hamiltonians and the zero-field splitting Hamiltonians—Survey of the CF=ZFS confusion in recent literature

The single transition ions in various crystals or molecules as well as the exchange coupled systems (ECS) of transition ions, especially the single molecule magnets (SMM) or molecular nanomagnets (MNM), have been extensively studied in recent decades using electron magnetic resonance (EMR), optical spectroscopy, and magnetic measurements. Interpretation of magnetic and spectroscopic properties of transition ions is based on two physically distinct types of Hamiltonians: the physical crystal field (CF), or equivalently ligand field (LF), Hamiltonians and the effective spin Hamiltonians (SH), which include the zero-field splitting (ZFS) Hamiltonians. Survey of recent literature has revealed a number of terminological confusions and specific problems occurring at the interface between these Hamiltonians (denoted CF (LF)↔SH (ZFS)). Elucidation of sloppy or incorrect usage of crucial notions, especially those describing or parameterizing crystal fields and zero field splittings, is a very challenging task that requires several reviews. Here we focus on the prevailing confusion between the CF (LF) and SH (ZFS) quantities, denoted as the CF=ZFS confusion, which consists in referring to the parameters (or Hamiltonians), which are the true ZFS (or SH) quantities, as purportedly the CF (LF) quantities. The inverse ZFS=CF confusion, which pertains to the cases of labeling the true CF (LF) quantities as purportedly the ZFS quantities, is considered in a follow-up paper. The two reviews prepare grounds for a systematization of nomenclature aimed at bringing order to the zoo of different Hamiltonians. Specific cases of the CF=ZFS confusion identified in the recent textbooks, review articles, and SMM (MNM)- and EMR-related papers are surveyed and the pertinent misconceptions are outlined. The consequences of the terminological confusions go far beyond simple semantic issues or misleading keyword classifications of papers in journals and scientific databases. Serious consequences include misinterpretation of data from a wide range of experimental techniques and, most recently, have lead to pitfalls and errors of substance bearing on understanding of physical properties. Clarification of the incorrect terminology may prevent further proliferation of the problems and confusions, and thus bringing about better understanding of the physical principles involved.

Chemical structures and electrical properties of atomic layer deposited HfO2 thin films grown at an extremely low temperature (≤100 °C) using O3 as an oxygen source

The properties of atomic layer deposited (ALD) HfO2 films grown at low temperatures (≤100°C) were examined for potential applications in flexible display and bioelectronics. A saturated ALD growth behavior was observed even at an extremely low temperature (30°C) due to the strong oxidizing potential of O3. However, HfO2 films grown at low temperatures showed a low film density and high impurity concentration, because the thermal energy during film growth was insufficient to remove ligands completely from Hf ions in precursor molecule. This resulted in low dielectric constant and high leakage current density of the films. Nevertheless, HfO2 film grown at 100°C using O3 gas with a high concentration (390g/Nm3) showed a tolerable impurity concentration with the dielectric constant of ∼16 and breakdown field of ∼4MV/cm, which are approximately two-thirds of those of HfO2 film grown at 250°C.

Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water

The functional forms of many RNAs have compact architectures. The placement of phosphates within such structures must be influenced not only by the strong electrostatic repulsion between phosphates, but also by networks of interactions between phosphates, water, and mobile ions. This review first explores what has been learned of the basic thermodynamic constraints on these arrangements from studies of hydration and ions in simple DNA molecules, and then gives an overview of what is known about ion and water interactions with RNA structures. A brief survey of RNA crystal structures identifies several interesting architectures in which closely spaced phosphates share hydration shells or phosphates are buried in environments that provide intramolecular hydrogen bonds or site-bound cations. Formation of these structures must require strong coupling between the uptake of ions and release of water.

Capture of an electron by ions in methionine and norleucine molecules

The relative cross sections of processes taking place when H+ and He2+ ions with an energy of 6z keV (z is the ionic charge) capture an electron from molecules of C5H11NO2S methionine (proteogenic amino acid) and C6H13NO2 norleucine (nonproteogenic amino acid) are measured by time-of-flight mass spectrometry (a methionine molecule transforms into a norleucine molecule by substituting the CH2 group for the S heteroatom). The fragmentation pattern of resulting molecular ions is established from correlation analysis of the detection times of all fragment ions. The results are compared with experimental data for fragmentation of the same molecules ionized by electrons and photons. In these amino acids, the pattern of molecular ion fragmentation is found to depend on the type of molecule ionization. However, the detachment cross section of the COOH neutral group or residue (neutral or charged) R of a side chain of the amino acid is invariably among the largest. The relative cross sections of capture with single and double ionization of molecules are measured.

Potencial Energy Functions & Properties of Some Hydride Molecules

I. IntroductionAlkali hydride molecules are chemically very simple compounds but due to their reactive nature, a very few physical properties of these molecules could be measured. As such the experimental information about them is not available in the literature. Owing to the non availability of the observed data for other practical applications the theoretical estimates of the various properties of these hydrides will be useful. In this connection several effects have already been taken up by different workers. The nature of forces which bind the atom or ions in the diatomic molecules is of fundamental importance in the fields of physico-chemical interest. Rittner 1 for the first time proposed a polarizable ion model for alkali halide molecules through which the interionic forces could be understood. Later on, Brumer & Karplus 2 modified the Rittner model known as truncated Rittner model or simply known as T-Rittner model given by,

Oligopeptidase B from Serratia proteamaculans. III. Inhibition analysis. Specific interactions with metalloproteinase inhibitors

Inhibition of the novel oligopeptidase B from Serratia proteamaculans (PSP) by basic pancreatic trypsin inhibitor, Zn2+ ions, and o- and m-phenanthroline was investigated. A pronounced effect of calcium ions on the interaction of PSP with inhibitors was demonstrated. Inversion voltamperometry and atomic absorption spectrometry revealed no zinc ions in the PSP molecule. Hydrophobic nature of the enzyme inhibition by o- and m-phenanthroline was established.

Structure Analysis of a New Psychrophilic Marine Protease

A new psychrophilic marine protease was found from a marine bacterium Flavobacterium YS-80 in the Chinese Yellow Sea. The protease is about 49 kD with an isoelectric point about 4.5. It consists of 480 amino acids and is homologous to a psychrophilic alkaline protease (PAP) from an Antarctic Pseudomonas species. The protein was purified from the natural bacterium fermented and crystallized. Its crystal structure (PDB ID 3U1R) was solved at 2.0 Å by Molecular Replacement using a model based on PAP, and was refined to a crystallographic Rwork of 0.16 and an Rfree of 0.21. The marine protease consists of a two domain structure with an N-terminal domain including residues 37–264 and a C-terminal domain including residues 265–480. Similar to PAP, the N-terminal domain is responsible for proteolysis and the C-terminal is for stability. His186, His190, His196 and Tyr226 are ligands for the Zn2+ ion in the catalytic center. The enzyme's Tyr226 is closer to the Zn2+ ion than in PAP and it shows a stronger Zn2+―Tyr-OH bond. There are eight calcium ions in the marine protease molecule and they have significantly shorter bond distances to their ligands compared to their counterparts in all three crystal forms of PAP. On the other hand, the loops in the marine protease are more compact than in PAP. This makes the total structure stable and less flexible, resulting in higher thermo stability. These properties are consistent with the respective environments of the proteases. The structural analysis of this new marine protease provides new information for the study of psychrophilic proteases and is helpful for elucidating the structure-environment adaptation of these enzymes.

X-ray diffraction study of Penicillium Vitale catalase in the complex with aminotriazole

The three-dimensional structure of the enzyme catalase from Penicillium vitale in a complex with the inhibitor aminotriazole was solved and refined by protein X-ray crystallography methods. An analysis of the three-dimensional structure of the complex showed that the inhibition of the enzyme occurs as a result of the covalent binding of aminotriazole to the amino-acid residue His64 in the active site of the enzyme. An investigation of the three-dimensional structure of the complex resulted in the amino-acid residues being more precisely identified. The binding sites of saccharide residues and calcium ions in the protein molecule were found.

Effect of Ionization on Infrared and Electronic Absorption Spectra of Methyl and Ethyl Formate in the Gas Phase and in Astrophysical H2O Ice: A Computational Study

This work reports infrared and electronic absorption spectra of trans and gauche conformers of neutral ethyl formate, trans and cis conformers of neutral methyl formate, their ions in the gas phase, and neutral ethyl and methyl formate in astrophysical H(2)O ice. The second-order Møller-Plesset perturbation (MP2) method with TZVP basis set has been used to obtain ground-state geometries. An influence of ice on vibrational frequencies of neutral ethyl and methyl formate was obtained using integral equation formalism polarizable continnum model (IEFPCM). Significant shift in vibrational frequencies for neutral methyl and ethyl formate when studied in H(2)O ice and upon ionization is observed. Rotational and distortion constants for neutral ethyl and methyl formate from this work are in excellent agreement with the available experimental values. Electronic absorption spectra of conformers of ethyl and methyl formate and their ions are obtained using time-dependent density functional method (TDDFT). The nature of electronic transitions is also identified. We suggested lines especially good to detect these molecules in interstellar medium. Using these lines, we can identify the conformers of ethyl and methyl formate in gas phase and H(2)O ice in interstellar medium. This comparative study should provide useful guidelines to detect conformers of ethyl and methyl formate and their ions in gas phase and neutral molecules in H(2)O ice in different astronomical environment.

Synthesis, Crystal Structures, and Magnetic Properties of Dinuclear and Hexanuclear Copper(II) Complexes with Cyclam-Based Macrocyclic Ligands Having Four Schiff-Base Pendant Arms

Abstract Reaction of a series of dodecadentate ligands (H4L), 1,4,8,11-tetrakis(salicylideneaminoethyl)-1,4,8,11-tetraazacyclotetradecane and its substituted derivatives, with copper(II) salts afforded dinuclear copper(II) complexes, [Cu2L], which were characterized by IR and UV–vis–NIR spectroscopy, and temperature dependence of magnetic susceptibilities (4.5–300 K). Single-crystal X-ray crystallography of these complexes revealed that each copper(II) ion is bound by the chelating of the two Schiff-base pendant arms outside the central tetraazacyclotetradecane ring forming a distorted square plane with an intramolecular Cu–Cu distance of 8.692(2)–8.949(2) Å. In accordance with the crystal structures, the magnetic interaction between the two copper(II) atoms is very weak. In the case of 1,4,8,11-tetrakis(3-methoxysalicylideneaminoethyl)-1,4,8,11-tetraazacyclotetradecane (H4tmsaec), a hexanuclear complex with a crystallographic inversion center, [Cu6(O2CCH3)8(tmsaec)], was isolated. In the asymmetric unit, one copper atom is bonded to one pendant arm and two copper atoms are bound to another pendant arm with the methoxy group of the Schiff-base moiety with the Cu–Cu distance of 3.096(1) Å, giving a novel system containing monodentate, bidentate, and bridging acetate ions in the same molecule. Magnetic susceptibility data shows that a weak antiferromagnetic interaction is operating between the closest two copper atoms.

Synthesis, structure, and luminescence properties of complex ZnLClb2 (L is 2-(3,5-dimethylpyrazol-1-yl)-4-methylquinoline)

A complex ZnLClb2 (L is 2-(3,5-dimethylpyrazol-1-yl)-4-methylquinoline) was synthesized. According to X-ray diffraction data, the Znp2+ ions in mononuclear molecules of the obtained complex coordinate two N atoms of the bidentate chelating ligand L and two Cl atoms. The coordination polyhedron Cl2Nb2 represents a distorted tetrahedron. In solid state at 300 K, the ligand L exhibits weak photoluminescence in the visible spectral range. The complex ZnLClb2 exhibits bright blue photoluminescence.

Coherent THz wave induced excitation in superionic conductors

Millimeter wave absorption spectra of silver halides doped silver phosphate glasses were measured using an intense coherent transition radiation. Two bands were observed at 8.4cm-1 and 6.3cm-1 in AgI doped AgPO3 glass and 8.7cm-1 and 6.1cm-1 in AgBr doped one. Small difference of peak positions between these glasses suggests that these absorption bands are concerned with a large number of silver ions in dopant molecules.

A systematic study of influence of ligand substitutions on the electronic structure and magnetic properties of Mn4single-molecule magnets

We present a density-functional theory study of the influence of ligand substitutions on the geometric structure, electronic structure, and magnetic properties of Mn4 single-molecule magnets (SMMs), in order to investigate the role of ligands in controlling these features, as well as in developing new SMMs and single-chain magnets (SCMs). Our results show that the peripheral ligands play an important role in controlling the magnetic ground-state of Mn4 SMMs. A new model is proposed to explain the spin state of manganese ions in Mn4 molecules. This model shows that the saving energy from distortion, which can be controlled by peripheral-ligand substitutions, plays a crucial role in determining the spin state of manganese ions in Mn4 molecules. The mechanism of strong exchange couplings between manganese ions in Mn4 SMMs is revealed. The strength of exchange-couplings between manganese ions in Mn4 SMMs as a function of their charge and spin state can be also controlled by substituting peripheral-ligands. The results demonstrate the possibilities of developing new Mn4-based SMMs. In addition, strong spin polarizations on peripheral ligands containing sp2-hybridized carbon sites show that using ligands containing sp2-hybridized carbon sites can enhance exchange couplings between Mn4 building blocks to develop new SMMs and SCMs which operate at high temperatures.

Polymer geometry and Li + conduction in poly(ethylene oxide)

We study the effect of molecular shape on Li + conduction in dilute and concentrated polymer electrolytes (LiI: P(EO) n (3 ⩽ n ⩽ 100)). We model the transport-diffusion of interacting Li + ions in the helical PEO molecule as Brownian motion in a field of electrical force. Our model demonstrates that ionic conductivity of the amorphous PE structure is increased by mechanical stretching due to the unraveling of loops in the polymer molecule and to increased order. The enhancement of the ionic conductivity in the stretch direction, observed in our Brownian simulations, is in agreement with experimental results. We find an up to 40-fold increase in the LiI P(EO) 7 conductivity, which is also in agreement with experimental results. The good agreement with experiment lends much credibility to our physical model of conductivity.

Accounting for ligand‐bound metal ions in docking small molecules on adenylyl cyclase toxins

The adenylyl cyclase toxins produced by bacteria (such as the edema factor (EF) of Bacillus anthracis and CyaA of Bordetella pertussis) are important virulence factors in anthrax and whooping cough. Co-crystal structures of these proteins differ in the number and positioning of metal ions in the active site. Metal ions bound only to the ligands in the crystal structures are not included during the docking. To determine what effect these "missing" metals have on docking results, the AutoDock, LigandFit/Cerius2, and FlexX programs were compared for their ability to correctly place substrate analogues and inhibitors into the active sites of the crystal structures of EF, CyaA, and mammalian adenylate cyclase. Protonating the phosphates of substrate analogues improved the accuracy of docking into the active site of CyaA, where the grid did not account for one of the three Mg2+ ions in the crystal structure. The AutoDock ranking (based on docking energies) of a test group of compounds was relatively unaffected by protonation of carboxyl groups. However, the ranking by FlexX-ChemScore varied significantly, especially for docking to CyaA, suggesting that alternate protonation states should be tested when screening compound libraries with this program. When the charges on the bound metal were set correctly, AutoDock was the most reliable program of the three tested with respect to positioning substrate analogues and ranking compounds according to their experimentally determined ability to inhibit EF.

Data and modeling of negative ion transport in gases of interest for production of integrated circuits and nanotechnologies

We review techniques to prepare, evaluate and apply sets of cross section and transport data for negative ions that are required for the modeling of collisional non-equilibrium plasmas used for processing of microelectronic circuits. We collect and discuss the transport coefficients and cross section sets.We have compiled data for negative ions in CF4 and CF4-related negative ions in rare gases. In addition, we consider data for F− and CF3− in rare gases. Furthermore, we analyze the cross sections of halogen negative ions in rare gases and other molecules. This is followed by the data for SF6 related ions in SF6 and in rare gases. The cross section for scattering of O− in O2 has been derived from the transport data and used to make calculations of the transport properties. Finally we give a brief discussion of the availability of the data for H− ions in H2. We have derived cross sections in several cases but the basic aim is to show the basic features of transport coefficients. In particular we discuss the need to represent properly some details such as the non-conservative nature of transport coefficients and the anisotropy of diffusion. Application of approximate theories and representations of cross sections are also discussed.