Characterization of aromatic-thiol π-type hydrogen bonding and phenylalanine-cysteine side chain interactions through ab initio calculations and protein database analyses

In this study, the aromatic-thiol π hydrogen bonding and phenylalanine-cysteine side chain interactions are characterized through both molecular orbital calculations on a C₆H₆-HSCH₃ model complex and database analyses of 609 X-ray protein structures. The aromatic-thiol π hydrogen bonding interaction can achieve a stabilization energy of 2.60 kcal mol^?1, and is stronger than the already documented aromatic-hydroxyl and aromatic-amino hydrogen bonds. However, the occurrence of the aromatic-thiol hydrogen bond is rather rare in proteins. This is because most of the thiol groups participate in the formation of either disulphide bonds or stronger S—H…O (or N) ‘normal’ hydrogen bonds in a protein environment. Interactions between the side chains of phenylalanine and cysteine residues are characterized as the phenyl(Phe)(HSCH₂-)(Cys) interaction. The bonding energy for such interactions is approximately 3.71 kcal mol-¹ and is achieved in a geometric arrangement with an optimal phenyl(Phe)-(HS-)(Cys) π-type hydrogen bonding interaction. The interaction is very sensitive to the orientation of the two lone electron pairs on the sulphur atom relative to the π electron cloud of the phenyl ring. Accordingly, the interaction configurations that can accomplish a significant bonding energy exist only within a narrow configurational space. The database analysis of 609 experimental X-ray protein structures demonstrates that only 268 of the 1620 cysteine residues involve such phenylalanine-cysteine side chain interactions. Most of these interactions occur in the form of π (aromatic)-lone pair(sulphur) attractions, and correspond to a bonding energy less than 1.5 kcal mol^?1. A few were identified as the aromatic-thiol hydrogen bond with a bonding energy of 2.0–3.6 kcal mol^?1.     

Infrared spectra of hydrogen impurities in BaTiO3 crystals

The IR spectra in the 2.8 μm region of the OH^? impurities in thick single domain crystals have been measured for different polarization geometries and various temperatures. Simple calculations of the Coulomb interactions between hydrogen and lattice ions show that these interactions are much more important than the hydrogen bonding ones for determining the positions of the hydrogen ions. The appearance of only one strong non-dichroic OH^? stretching line is due to an almost equal population of the proton axial sites. The side bands are interpreted as combinations of the stretching mode with a low-frequency translational mode. The large broadening of the main line just above T_c supports the model which attributes a considerable order—disorder character to the ferroelectric phase transition.     

99Ru Mössbauer spectroscopic study on salts of ruthenocene with halogens

⁹⁹Ru Mössbauer spectra at 5 K have been measured on samples of salts of ruthenocene with halogens, expressed as [Ru(C₅H₅)₂X]Y (X=Cl, Br, Y=PF₆, and X=1, Y=13). The values of both the isomer shift and the quadrupole splitting of these salts with halogens are larger compared to those of ruthenocene. It is concluded that ruthenocene gives salts having direct chemical bonding between Ru and Cl, Br, or I, and that the Ru atom in each salt is in a higher oxidation state than 2+ in ruthenocene.     

鼓型CoB16-团簇电子结构的探索：罕见的Co(-1)氧化态

本文发现CoB₁₆^-团簇由两个对称、上下错位相连的B₈环和位于中心的Co原子组成,它代表了金属掺杂硼纳米管结构的潜在雏形,这一发现为设计一维金属-硼纳米结构提供了机会. 本文报道了CoB₁₆^-新的实验光电子能谱,并采用量子化学方法对其电子结构和化学成键特性进行了详细的电子结构分析,为进一步了解金属掺杂硼纳米管结构的化学键和稳定性提供了深入的见解. 有趣的是,发现该类体系的中心Co原子具有异常低的氧化态,即负一价钴(-1). 因此中性CoB₁₆分子可以被视为配体到金属的电荷转移化合物(Co^-@BB₁₆⁺). 研究表明,掺杂金属和硼管之间的相互作用来源于共价和静电作用的相互协调,硼元素低的电负性使得硼团簇成为形成各种低价态化合物的重要化学配体.     

Reflection spectra of (alkali metal,thallium (I), silver (I)) iridium (IV) hexachlorides

While the effect of rubidium and caesium ions in solid salts of IrCl₆ ^-- is a shift to lower wave-numbers, comparable to that occurring in organic solvents relative to water, the dark blue silver (I) and thallium (I) salts have a new, broad band in the red. Mixed crystals of Cs₂IrCl₆ and Tl₂IrCl₆ are prepared, and the absorption spectra are discussed in terms of a tendency to ‘ferroelectric rattling’ and strong covalent bonding of Ag and Tl. Analogous cases are pointed out in solid salts of other 5d-hexahalides.     

Engineering the Internal Structure of Magnetic Silica Nanoparticles by Thermal Control

Calcination of hydrated iron salts in the pores of both spherical and rod‐shaped mesoporous silica nanoparticles (NPs) changes the internal structure from an ordered 2D hexagonal structure into a smaller number of large voids in the particles with sizes ranging from large hollow cores down to ten nanometer voids. The voids only form when the heating rate is rapid at a rate of 30 °C min^?1. The sizes of the voids are controlled reproducibly by the final calcination temperature; as the temperature is decreased the number of voids decreases as their size increases. The phase of the iron oxide NPs is α‐Fe₂O₃ when annealed at 500 °C, and Fe₃O₄ when annealed at lower temperatures. The water molecules in the hydrated iron (III) chloride precursor salts appear to play important roles by hydrolyzing Si? O? Si bonding, and the resulting silanol is mobile enough to affect the reconstruction into the framed hollow structures at high temperature. Along with hexahydrates, trivalent Fe³⁺ ions are assumed to contribute to the structure disruption of mesoporous silica by replacing tetrahedral Si⁴⁺ ions and making Fe? O? Si bonding. Volume fraction tomography images generated from transmission electron microscopy (TEM) images enable precise visualization of the structures. These results provide a controllable method of engineering the internal shapes in silica matrices containing superparamagnetic NPs.     

Chemical structure of iodine-doped polyisoprene

A nonconjugated conducting polymer (1,4-rans-polyisoprene) at different iodine doping levels has been studied with the 27.7-keV Mössbauer resonance of¹²⁹I. At the light doping level, almost all iodines are covalently bonding to the carbon atoms, breaking the double bonds of the main chain. At the medium doping level, other iodine species are found, which are idendified as anion species, l^?, l ₃ ^? and l ₃ ^? .At the heavy doping level, polyiodide anions, l ₃ ^? and l ₅ ^? , increase as compared to the covalently bonding iodine atoms and addtionally molecular iodine l₂ exists.     

Spin-orbit coupling in nitrite ion and nitrite salts

The absorption intensity of the³B₁ ¹A₁ transition of nitrite salts of the non-transition metals is markedly dependent on the metal counterion and is causative of the yellow-orange colors of the heavier-metal salts. It is assumed that spin-orbit coupling is responsible for this phenomenon; this assumption is investigated here using semi-empirical one-electron calculations and is validated. The subjects of covalent bonding in metal salts, charge transfer transitions in such systems and the S _j S ₀ electronic spectroscopy of nitrite salts are also investigated.This work was supported by contracts between the United States Atomic Energy Commission — Biology Branch and the United States Air Force with the Louisiana State University.     

Infrared and Raman spectroscopic studies of the charge localization in one‐dimensional organic metals (DMtTTF)2X (X = ReO4, ClO4) with regular organic stacks

A novel selective synthesis of the unsymmetrically substituted tetrathiafulvalene dimethyltrimethylene‐tetrathiafulvalene (DMtTTF) is described together with its electrocrystallization to the known conducting mixed‐valence ClO₄^– and ReO₄^– salts. Infrared (IR) and Raman spectra of the two isostructural quasi‐one‐dimensional cation radical salts (DMtTTF)₂X (X = ReO₄^–, ClO₄^–) are investigated as a function of temperature (T = 5–300 K). At ambient temperature, these salts show metallic‐like properties and below T_ρ = 100–150 K, they undergo a smeared transition to semiconducting state. To study this charge localization, we measured temperature dependence of polarized IR reflectance spectra (700–16 000 cm^–1) and Raman spectra (150–3500 cm^–1, excitation λ = 632.8 nm) of single crystals. For both compounds, the Raman data and especially the bands related to the C=C stretching vibration of the DMtTTF molecule show that the charge distribution on molecules is uniform down to the lowest temperatures. Similarly, IR data confirm that down to the lowest temperatures, there is neither charge ordering nor important modification of the electronic structure. However, the temperature dependence of Raman spectra of both salts reveals a regime change at about 150 K. Additionally, using Density Functional Theory (DFT) methods, the normal vibrational modes of the neutral DMtTTF⁰ and cationic DMtTTF⁺ species and also their theoretical IR and Raman spectra were calculated. The theoretical data were compared with the experimental IR and Raman spectra of neutral DMtTTF⁰ molecule. Copyright © 2013 John Wiley & Sons, Ltd.     

The equilibrium and kinetics of intermolecular hydrogen bonding in nitroarene anion radical–alcohol system: 1,3‐dinitro‐benzene anion radical – R–OH (R═CH3–, C2H5–, (CH3)2 CH–)

To explore the possibility of hydrogen bonding of a stable anion radical with DNA – component sugar, hormones, steroid, and so on (through hydroxyl group), as a first step, the possibility of hydrogen bonding of 1,3‐dinitrobenzene anion radical (1,3‐DNB^??) with aliphatic alcohols was studied. It was found that 1,3‐DNB^?? anion radical undergoes hydrogen bonding with alcohols: methanol, ethanol, and 2‐proponal. The hydrogen‐bonding equilibrium constant K_eq and the (hydrogen‐bonding) rate constants k₂ were evaluated through the use of linear scan and cyclic voltammetry theory and techniques. The K_eq was found to be in the range of 1.4–6.0 m ^?1, whereas the rate constants k₂ were found to be in the range of 1.5–3.6 m ^?1 s^?1, depending upon the hydrogen‐bonding agent and the equation used for the calculation of the rate constants. The hydrogen‐bonding number n was found to be around 0.5 or 1.0. The implication of this study in, for example, the replication of DNA, the prevention of the formation of super oxide, and so on is discussed. Copyright © 2012 John Wiley & Sons, Ltd.     

Energy dependence of possible charge-independence- and charge-symmetry-breaking effects inNN 3 P J interactions from three-nucleon continuum studies

A recent study of charge-independence-and charge-symmetry-breaking effects in the³ P _J nucleon-nucleon interactions has been extended down to 5 MeV nucleon energy. It has been found that charge-independence-breaking effects are almost energy independent in the entire energy range investigated. Possible charge-symmetry-breaking effects in the³ P _J NN interactions exhibit a rather strong energy dependence at very low energies.     

Effect of oxygen content and charge on the structure,stability and optoelectronic properties of yttrium oxide clusters

The electronic and geometrical structures of neutral and charged YOn (n=2–12) clusters have been investigated using density functional theory (DFT) with generalized gradient approximation. The oxygen atom in YOn has been found to be in oxo, peroxo and in superoxo forms. The geometrical structures and topologies of small size anionic clusters resemble that of neutral clusters. Yttrium showed higher coordination number than scandium. Computed results reveal the existence of YO₁₀ cluster to have a penta-peroxo oxygen with a homoleptic Y(η² –O₂)₅ geometrical configuration. The HOMO–LUMO gaps decrease with increasing n due to the increase in 2p orbital population of oxygen atoms. It has been shown that in these clusters bonding are predominantly ionic in nature and anions are thermodynamically more stable, due to the charge delocalization between the metal atom and oxygen ligands. YO₁₀⁺ and YO₁₂⁺ were found to be highly exothermic to release one and two oxygen molecules, while YO₁₁⁺ dissociates though the ozonide dissociation channel. Computed absorption spectra of small clusters are mainly contributed by yttrium metal d and s valence orbitals. The absorbance spectra, shifts towards lower energy with cluster size increase, while charge has no substantial effect on the absorption spectrum.     

SiC bonding in ( C 60 ) n Si m clusters

This paper deals with a new type of SiC bonding where silicon atom seems to bridge C₆₀ molecules. We have studied films obtained by deposition of (C₆₀)_nSi_m clusters prepared in a laser vaporization source. Prior deposition, free ionized clusters were studied in a time-of-flight mass spectrometer. Mixed clusters (C₆₀)_nSi_m were clearly observed. Abundance and photofragmentation mass spectroscopies revealed the relatively high stability of the (C₆₀)_nSi _n ⁺ , (C₆₀)_nSi _{n - 1} ⁺ and (C₆₀)_nSi _{n - 2} ⁺ species. This observation is in favor of the arrangement of these complexes as polymers where the C₆₀ cages may be bridged by a silicon atom. Free neutral clusters are then deposited onto substrate making up a nanogranular thin film (≃ 100 nm). The film is probed by Auger and X-ray photoemission spectroscopies, but above all by surface enhanced Raman scattering. The results suggest an unusual chemical bonding between silicon and carbon and the environment of the silicon atom is expected to be totally different from the sp³ lattice: ten or twelve carbon neighbors might surround silicon atom. The bonding is discussed to the light of the so-called fullerene polymerization as observed for pure fullerite upon laser irradiation. This opens a new route for bridging C₆₀ molecules together with an appreciable energy bonding, since the usual van der Waals bonding in fullerite could be replaced by an ionocovalent bond. Such an assumption must be checked in the future by XAS and EXAFS experiments. Received 15 November 2000     

Crystal-host Gd0.5Lu0.5VO4 for Ln3+-lasants: a new high-gain many-phonon χ(3)-active tetragonal vanadate—SRS spectroscopy and nonlinear-laser effects

We found that tetragonal Gd_0.5Lu_0.5VO₄??known as host-crystal for Ln³⁺-lasants??is an attractive optical material for Raman laser converters. We discovered and investigated its almost sesqui-octave Stokes and anti-Stokes lasing comb resulting from four SRS-promoting vibration modes in combination with cascaded and cross-cascaded many-phonon ??⁽³⁾-nonlinear interactions. Furthermore, estimations of the steady-state Raman gain coefficient have been performed.     

Inclusive neutral kaon production in 70 GeV/c K+p interactions

The inclusive production of neutral kaons in 70 GeV/c K⁺p interactions is studied with the CERN BEBC bubble chamber. The (semi-)inclusive cross sections are interpreted in terms of the various strangeness channels leading to neutral kaon production. The invariant inclusive cross section for kaon production is studied as a function of p_t² and the Feynman variable x. The latter distributions are considered both “raw” and corrected for the presence of K⁰'s resulting from K¹ decay. They are compared with the predictions expected from the Regge-Mueller formalism, the recombination model and fragmentation models.     

Valence bond analysis of the bonding in transition metal compounds: the RuNO group in nitrosyl complexes

The ab initio and semi-empirical configuration interaction wave functions of ruthenium complexes [RuL₅(XY) ^q (L &; = NH₃, Cl^?, CN^?, XY &;= N₂, CO) are presented in the form of linear combinations of the valence bond (VB) structures, each structure being referred to some covalent or ionic model of the bonding in the M-XY group. The results of this VB analysis showed that [RuL₅(NO)] ^q complexes can be described as compounds of Ru(III) and neutral NO⁰ with a covalent π-bond in addition to the usual coordination bond.     

EPR and Magnetic Susceptibility of Na2O–CuO–P2O5 Glasses

Abstract

(50?x/2)Na₂O–xCuO–(50?x/2)P₂O₅ glasses (x=1, 5, 15, or 30 mol%) have been prepared and characterized by electron paramagnetic resonance (EPR) and magnetic susceptibility measurements. The shape of the Cu²⁺ EPR spectrum depends on the Cu content, and the corresponding computer simulations suggest that the Cu²⁺ ions occupy two different sites in these glasses: one of them is preponderant at low Cu content and the other is preponderant at high content, in which the Cu²⁺–Cu²⁺ interactions are more important. From EPR parameters, it was found that for the site at low content, the covalency of copper ion bonding with the surrounding ligands is appreciable. The magnetic susceptibility data appear to follow the Curie–Weiss law (χ=C/(T?θ_p)) with negative paramagnetic Curie temperature θ_p indicating antiferromagnetic interactions between Cu²⁺ ions that are more significant in the samples with high Cu content, in agreement with EPR results.     

A light neutral intermediate vector boson without large e+e−→ μ+μ− asymmetries

An effective SU(2)×U(1)×U(1)' electroweak theory is shown to permit the occurence of a pair of neutral intermediate vector bosons with masses 40 GeV?m_light?70 GeV, m^W.S._Z⁰<m_heavy?100 GeV. Neutrino neutral current interactions are shown to be the same as in the standard electroweak model, and e⁺e^?→μ⁺μ^? forward-backward asymmetries are within experimental bounds for m_light?40 GeV.     

Influence of Tetra Alkyl Ammonium Cation on Thermo-Physical Properties of N,N-Dimethyl Formamide with 1,4-Dioxane at Different Temperatures

Ultrasonic technique, transport properties and related acoustical parameters of 1,4-dioxane and N,N-dimethyl formamide were prepared of different % compositions at variable temperatures using tetra alkyl ammonium iodide salts (R₄NI) of 0.14 M, to investigate inter-ionic interactions, molecular interactions, molecular rearrangement, molecular association etc. The densities were measured by using magnetic float densitometer. Transport properties provide a deep and meaningful insight of various interactions taking place between the binary liquid mixtures with salts. We have observed the influence of small as well as large alkyl chain length (R₄N⁺), and extract the information with respect to various kinds of intermolecular interactions such as dipole-dipole, dipole-induced dipole, solute-solvent, dispersive type and H-bonding interaction between the components. Such observations in the presence of specific molecular interactions of binary solutions and structural effects were analyzed on the basis of measured and derived thermo-dynamical parameters.