Trigonally-compressed octahedral geometry of hexaamminecobalt(III) complex cation in aqueous solution investigated from the electronic spectra

Electronic spectra of hexaamminecobalt(III) complex cation in aqueous solution were analyzed to obtain spectral components. Subsequently, based on the spectral components, the coordination geometry around the cobalt(III) ion was investigated, using the reverse angular overlap model method. The result indicates that the geometry is a trigonally compressed octahedron with the polar angle of 57.9?±?1.0° under D_3d symmetry, where the polar angle is the angle between the trigonal axis and the Co–N bond. From this angle, the top and side N–Co–N bond angles are calculated as 94.4° and 85.6°, respectively. The density functional theory computation supported this trigonally compressed structure in aqueous solution.     

Thermal Effect on Aequorea Green Fluorescent Protein Anionic and Neutral Chromophore Forms Fluorescence

The emission behaviour of Aequorea green fluorescent protein (A-GFP) chromophore, in both neutral (N) and anionic (A) form, was studied in the temperature range from 20 °C to 75 °C and at pH = 7. Excitation wavelengths of 399 nm and 476 nm were applied to probe the N and A forms environment, respectively. Both forms exhibit distinct fluorescence patterns at high temperature values. The emission quenching rate, following a temperature increase, is higher for the chromophore N form as a result of the hydrogen bond network weakening. The chromophore anionic form emission maximum is red shifted, upon temperature increase, due to a charge transfer process occurring after A form excitation.     

Carbon isotopic signature reveals the geographical trend in methane consumption and production pathways in alpine ecosystems over the Qinghai–Tibetan Plateau

On the Qinghai–Tibetan Plateau, isotopic signatures in soil–atmosphere CH₄ fluxes were investigated in nine grasslands and three wetlands. In the grasslands, the fractionation factor for soil CH₄ uptake, α_soil, was much smaller than the usually reported value of 0.9975–1.0095. Stepwise multiple variation analysis indicates that α_soil is higher for higher soil water contents but is lower for higher C/N ratios of soil surface biomass. In the three wetlands, the soil-emitted δ¹³C–CH₄ was similar (?55.3?±?5.5?‰ and ?53.0?±?5.5?‰) in two bogs separated by >1000?km but was lower (?63.4?±?6.3?‰) in a marsh. Environmental factors related to intrasite variations in soil-emitted δ¹³C–CH₄ include the soil C/N ratio, oxidation–reduction potential, soil C concentration and soil water contents. Geographical isotopic surveys revealed environmental constraints on the CH₄ consumption pathways in grasslands and the biome type-specific consistency in CH₄ production pathways in wetlands.     

Molecular physiology of rhodopsin: Computer simulation

Computer simulation is used for comparative investigation of the molecular dynamics of rhodopsin containing the chromophore group (11-cis-retinal) and free opsin. Molecular dynamics is traced within a time interval of 3000 ps; 3 × 10⁶ discrete conformational states of rhodopsin and opsin are obtained and analyzed. It is demonstrated that the presence of the chromophore group in the chromophore center of opsin influences considerably the nearest protein environment of 11-cis-retinal both in the region of the β-ionone ring and in the region of the protonated Schiff base bond. Based on simulation results, a possible intramolecular mechanism of keeping rhodopsin as a G-protein-coupled receptor in the inactive state, i.e., the chromophore function as an efficient ligand antagonist, is discussed.     

Homo‐Diels–Alder reaction of a very inactive diene,bicyclo[2,2,1]hepta‐2,5‐diene,with the most active dienophile, 4‐phenyl‐1,2,4‐triazolin‐3,5‐dione. Solvent,temperature, and high pressure influence on the reaction rate

Solvent, temperature, and high pressure influence on the rate constant of homo‐Diels–Alder cycloaddition reactions of the very active hetero‐dienophile, 4‐phenyl‐1,2,4‐triazolin‐3,5‐dione (1), with the very inactive unconjugated diene, bicyclo[2,2,1]hepta‐2,5‐diene (2), and of 1 with some substituted anthracenes have been studied. The rate constants change amounts to about seven orders of magnitude: from 3.95^.10^?3 for reaction (1+2) to 12200 L mol^?1 s^?1 for reaction of 1 with 9,10‐dimethylanthracene (4e) in toluene solution at 298 K. A comparison of the reactivity (ln k₂) and the heat of reactions (?_r‐nH) of maleic anhydride, tetracyanoethylene and of 1 with several dienes has been performed. The heat of reaction (1+2) is ?218 ± 2 kJ mol^?1, of 1 with 9,10‐dimethylanthracene ?117.8 ± 0.7 kJ mol^?1, and of 1 with 9,10‐dimethoxyanthracene ?91.6 ±0.2 kJ mol^?1. From these data, it follows that the exothermicity of reaction (1+2) is higher than that with 1,3‐butadiene. However, the heat of reaction of 9,10‐dimethylanthracene with 1 (?117.8 kJ mol^?1) is nearly the same as that found for the reaction with the structural C=C counterpart, N‐phenylmaleimide (?117.0 kJ mol^?1). Since the energy of the N=N bond is considerably lower (418 kJ/bond) than that of the C=C bond (611 kJ/bond), it was proposed that this difference in the bond energy can generate a lower barrier of activation in the Diels–Alder cycloaddition reaction with 1. Linear correlation (R = 0.94) of the solvent effect on the rate constants of reaction (1+2) and on the heat of solution of 1 has been observed. The ratio of the volume of activation (?V^≠) and the volume of reaction (?V_r‐n) of the homo‐Diels–Alder reaction (1+2) is considered as “normal”: ?V^≠/?V_r‐n = ?25.1/?30.95 = 0.81. Copyright © 2012 John Wiley & Sons, Ltd.     

Isotope (δ13C, δ15N, δ2H) diet–tissue discrimination in African grey parrot Psittacus erithacus: implications for forensic studies

Diet–tissue isotopic relationships established under controlled conditions are informative for determining the dietary sources and geographic provenance of organisms. We analysed δ¹³C, δ¹⁵N, and non-exchangeable δ²H values of captive African grey parrot Psittacus erithacus feathers grown on a fixed mixed-diet and borehole water. Diet–feather Δ¹³C and Δ¹⁵N discrimination values were +3.8?±?0.3?‰ and +6.3?±?0.7?‰ respectively; significantly greater than expected. Non-exchangeable δ²H feather values (?62.4?±?6.4?‰) were more negative than water (?26.1?±?2.5?‰) offered during feather growth. There was no positive relationship between the δ¹³C and δ¹⁵N values of the samples along each feather with the associated samples of food offered, or the feather non-exchangeable hydrogen isotope values with δ²H values of water, emphasising the complex processes involved in carbohydrate, protein, and income water routing to feather growth. Understanding the isotopic relationship between diet and feathers may provide greater clarity in the use of stable isotopes in feathers as a tool in determining origins of captive and wild-caught African grey parrots, a species that is widespread in aviculture and faces significant threats to wild populations. We suggest that these isotopic results, determined even in controlled laboratory conditions, be used with caution.     

Seasonal variation in natural abundance of δ13C and 15N in Salicornia brachiata Roxb. populations from a coastal area of India

High and fluctuating salinity is characteristic for coastal salt marshes, which strongly affect the physiology of halophytes consequently resulting in changes in stable isotope distribution. The natural abundance of stable isotopes (δ¹³C and δ¹⁵N) of the halophyte plant Salicornia brachiata and physico-chemical characteristics of soils were analysed in order to investigate the relationship of stable isotope distribution in different populations in a growing period in the coastal area of Gujarat, India. Aboveground and belowground biomass of S. brachiata was collected from six different populations at five times (September 2014, November 2014, January 2015, March 2015 and May 2015). The δ¹³C values in aboveground (?30.8 to ?23.6?‰, average: ?26.6?±?0.4?‰) and belowground biomass (?30.0 to ?23.1?‰, average: ?26.3?±?0.4?‰) were similar. The δ¹³C values were positively correlated with soil salinity and Na concentration, and negatively correlated with soil mineral nitrogen. The δ¹⁵N values of aboveground (6.7–16.1?‰, average: 9.6?±?0.4?‰) were comparatively higher than belowground biomass (5.4–13.2?‰, average: 7.8?±?0.3?‰). The δ¹⁵N values were negatively correlated with soil available P. We conclude that the variation in δ¹³C values of S. brachiata was possibly caused by soil salinity (associated Na content) and N limitation which demonstrates the potential of δ¹³C as an indicator of stress in plants.     

Conformational fluctuations in a green fluorescent protein-like Akane family protein: a high-pressure fluorescence study at 0.1–700 MPa

ABSTRACT

We have investigated conformational fluctuations in a new green fluorescent protein(GFP)-like protein rb-Akane found in a red-brown-colored octocoral, Scleronephthya gracillima (Kuekenthal)), with high pressure fluorescence spectroscopy at 0.1–700?MPa. Besides the green fluorescence at 510?nm, two red fluorescence peaks are observed at 590 and 629?nm, the relative intensity of which varies reversibly with pressure. The phenomenon is interpreted as representing the cis–trans isomerization of the chromophore accompanied by the conformational transition between two sub-states of the red fluorescence form of rb-Akane. The two sub-states are separated only marginally in free energy (ΔG⁰?=?1.9?±?0.4?kJ?mol^?1), but significantly in partial molar volume (ΔV⁰?=??19.8?±?1.4?ml?mol^?1) at 0.1?MPa (pH 7.5, 25°C). Above 500?MPa, the fluorescence at λ_max 629?nm undergoes another reversible change with pressure, showing the onset of unfolding.     

Accurate determination of the 13C-12C+n spectroscopic factor

We have measured ¹²C-¹³C elastic cross sections at 12 MeV between 40°–140° in 1° steps to ±1%. The observed oscillatory interference between Coulomb scattering and the neutron transfer process is analyzed using exact finite-range DWBA, and a model-independent value of C² = 2.55±0.10 for the asymptotic normalization of the $\text{1}\text{p}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$ neutron wave function in ¹³C is obtained. Using radial wave functions determined by elastic electron scattering the spectroscopic factor is found to be S = 0.81±0.04.     

Comparative analysis of sensory rhodopsin II structures in complex with a transducer and without it

Sensory rhodopsin II (NpSRII) is a heptahelical transmembrane protein containing the retinal chromophore. In complex with another membrane protein, i.e., NpHtrII transducer, NpSRII transmits a signal into a cell, initiating negative phototaxis of Natronobacterium pharaonis. In the absence of a transducer, rhodopsin II can work as a proton pump similar to bacteriorhodopsin. The main objective of this study is to comparatively analyze receptor structures in complex with the transducer and without it to understand the mechanism of the protein switching function. Diffraction data for sensory rhodopsin II crystals grown in the lipidic cubic phase were obtained at the synchrotron x-ray source. In this paper, we present a new NpSRII structure with a resolution of 2.1 Å and the results of a comparative analysis of the obtained NpSRII structure with our previously published data on the NpSRII/NpHtrII complex structure and with two NpSRII structures without a transducer, previously published in the literature.     

Carbon-13 Kinetic Isotope Effects in the Decarbonylation Of Liquid Formic Acid in Water Solution

Abstract

Carbon-13 kinetic isotope effects (¹³C KIEs) in the decarbonylation of formic acid diluted with water 1:1 (V:V) has been studied in the 130–181°C temperature interval in sealed vacuum all glass reactions vessels. The experimental ¹³C KIEs are higher than the ¹³C KIEs values extrapolated from low 50–100°C temperature interval ¹³C KIEs observed in the decarbonylation of water free liquid formic acid but less than ¹³C KIEs expected theoretically assuming the complete carbon—oxygen (¹³C[sbnd]¹⁶O) bond rupture in the transition state. For instance the (k₁₂/k₁₃) KIE found in this study is 1.0375 at 170.2°C while the “full” ¹³C KIE is expected to be 1.0429 at this temperature. The ¹³C KIE extrapolated to 170.2°C from the low temperature data published earlier is 1.0299. - The Arrhenius activation energy for the decarbonylation of formic acid in 1:1 water solution E = 31.3 kcal/mol is by 6 kcal/mol higher than that which was obtained with 99,9% pure formic acid (E = 25,660 kcal/mol). The entropy of activation ΔS ^≠ increased from -21.4 e.u. (pure formic acid) to -15.3 e.u. in the decarbonylation of formic acid diluted with water 1:1. The increases of the enthalpy of activation, of the entropy of activation and partly of the carbon-13 kinetic isotope effect observed in the decarbonylation of formic acid in water solution have been rationalized by suggesting isotopic equilibria interfering the pure kinetic fractionation of ¹³C and intervention of the water molecules into the process of transfer of protons to the formic acid molecules lowering the absolute rate of their decomposition.     

A theoretical conformational study on the structural parameters involved in the ring strain of exo-unsaturated four-membered heterocycles,Y = CCH2CH2X

The effect of ring-puckering angle on the structural parameters (bond lengths and angles) involved in the ring strain of a series of four-membered heterocycles (1–16) was theoretically demonstrated by using the ab initio methods MP2 and HF, and the DFT methods PBE1PBE, B3LYP, SVWN5 with 6-31+G(d,p) as basis set. The results revealed that the bonds within the ring (C–X and C–C) are the most sensitive to puckering angle changes. The variation of the C–X and C=Y bond lengths as function of puckering angle are determined by a balance between the 1,3 repulsive interactions and the electronic nature of the heteroatoms X and Y. Particularly, for azetidines and phosphetanes, the C–X and C=Y bond lengths exhibit a major increase at axial conformations. In general, the C–C bond length decreases with the puckering angle for all heterocycles. While the heteroatom–H bonds (in the ring skeleton) are very sensitive to geometric changes, exhibiting an increasing behaviour for equatorial conformations and a decreasing behaviour for axial conformations highly puckered (? > ?20°). The C–X–C angle decreases monotonically with the puckering angle, increasing the Baeyer strain on the studied molecules. Finally, all methods predicted a similar behaviour for the studied parameters as function of the puckering angle, although some smaller differences in the predictions of their respective values, especially at HF level, were observed.     

Structural studies of tetrachloride liquids

The differential cross-sections for neutron scattering from liquid carbon tetrachloride have been measured with the TSS instrument at the Harwell Electron Linac. Data were taken at seven different scattering angles for a wavelength range of 0·2–3·5 Å. The observed diffraction patterns at high momentum transfer (> 8–30 Å^-1) have been analysed in terms of the molecular form factor f ₁(Q). It was found that the oscillation amplitudes could be satisfactorily described only by introducing an energy-dependent term into the Debye-Waller factors of the form factor. The f ₁(Q) data were fitted with a four-parameter function for measurements at scattering angles of 150°, 90° and 58°. The carbon-chlorine bond length parameter was accurately defined in all cases and had a mean value of 1·766 ± 0·002 Å. The inclusion of an anharmonicity constant in the form factor gave an improved χ²-fit to the data with an increased value of 1·770 ± 0·002 Å for the bond length. The results are in excellent agreement with other measurements and show the importance of pulsed neutron techniques for molecular structure studies of disordered materials.     

Variable-Temperature and High-Pressure Micro-Raman Spectra of Inorganic Artists' Pigments: Crystalline Wulfenite,Lead(II) Molybdate(VI), PbMoO4

Variable-temperature (?150°C to 600°C) and high-pressure (up to ～5 GPa) micro-Raman spectra have been obtained for the mineral wulfenite [lead(II) molybdate(VI), PbMoO₄], a main constituent of the artists' pigment, orange molybdate. The spectra were quite similar in both the temperature and the pressure studies, except for broadening and shifting of some peaks. No phase changes were detected, although there is possibly some amorphization beginning at ～600°C. The photoacoustic IR spectrum in the 1950–450 cm^?1 region is reported for characterization purposes. The long-term stability of PbMoO₄ with respect to extreme changes in both temperature and pressure illustrates the importance of orange molybdate in artwork and protective coatings.     

A study of electromigration of nickel in lead

The steady state method was used to study the electromigration of ⁶³Ni in Pb. For the temperature range 180–290°C, and Ni concentration range 0.1–1000 ppm, Ni migrates toward the anode. For dilute samples (0.1 ppm Ni) the effective charge varies linearly with the inverse resistivity from ?6.75 at 188°C to ?4.97 at 289°C. The 1/ρ dependence is given by $\text{Z1 = (1.4 ± 0.3)?(288 ± 13)× 10}{}^{\mathrm{?6}}\text{/ρ}$. The effective charge is a function of the Ni concentration, increasing in magnitude with increasing concentration. For 1000 ppm Ni, |Z1| exhibits a sharp maximum around 260°C; below 230°C electromigration takes place at a much slower rate, probably due to precipitation.     

The structure factor for liquid bromine by neutron diffraction

Thermal neutrons from steady-state (reactor) and pulsed (linac) neutron facilities have been used to study the structure factor for liquid bromine at 20°C, covering a wide range of values (0·6-35 Å^-1) of the momentum transfer (?Q). The diffraction pattern at high Q-values (>10 Å^-1) gives information on the structural properties of the individual molecules but detailed interpretation is complicated by the vibrational motion which causes a systematic variation in the periodic oscillations of the molecular form-factor. An internuclear distance (bond length) of 2·28 ± 0·01 Å is found to be suitable for data at lower Q-values and has been used in the analysis of the liquid structure. The results show that some form of orientational correlation between molecules must be present and the nuclear (atom) pair correlation function is split into two peaks for the coordination shell corresponding to nearest-neighbour molecules. The results are compared with other studies of liquid bromine and similar neutron experiments for liquid nitrogen and liquid oxygen.     

Influence of Solution Acidity on Structure of Actinocin Derivatives and Their Affinity to DNA Studied as a Function of pH by Raman Spectroscopy

An important problem of molecular biophysics is the influence of pH and ionic strength of a solution on chemical structures and charge of biologically active substances. By means of pH titration and Raman spectroscopy methods, the influence of solution acidity on structural changes of actinocin derivatives was investigated, analogues to antitumor antibiotic actinomycin D. It has been shown that these ligands have different values of cation charges in neutral solutions. From analysis of Raman spectra, it was concluded that protonation of nitrogen atom and amino group of the phenoxazone ring starts only at pH < 3.5. It was shown that protonation of actinocin derivative with two amide groups (diaminoactinocin) occurred in two steps. Corresponding protonation constants for diaminoactinocin (log k ₁ = 6.9 ± 0.5 and log k ₂ = 5.3 ± 0.1) and for partially protonated actinocin derivative with three methylene groups in the side chains (log k = 5.3 ± 0.1) were obtained. Characteristic frequencies of Raman spectra for the basic functional C=O, C2–NH₂, C–C=C, and –N=C groups of phenoxazone chromophore of actinocin derivatives in protonated and nonprotonated states were determined. The different affinities of binding of variously charged ligands to DNA have also been demonstrated.     

The exciton absorption in deformed germanium

Absorption spectra at 77° K near the direct (κ = 0) exciton transition are reported for deformed and undeformed single-crystal films of n-type Ge oriented on (111); Elliott's theory is applied. The optical width of the forbidden band for this transition is found as E_{g 0} = (0.8821 ±±0.0002) eV, while the exciton binding energy is found as E_ex(0) = = (0.0016±0.0003) eV for undeformed Ge at 77 ° K. The mean temperature coefficient of E_g for κ = 0 in the range 77 °–297 ° K is (dE_g/ /dT)_p =?3.50 · 10^?4 eV/deg. The effects of thermoelastic deformation on the exciton spectrum give (dE_g/dT)_d = (?1.5±0.1) · 10^?4 eV/deg. The half-width σ ≈ 5 · 10^?4 eV of the exciton peak gives the exciton lifetime as gt ≥ 10^?12 sec.     

Metal hydrides as sodium bond acceptors: hydride-sodium bond in the XH ··· NaH (X = HBe,LiBe, NaBe,HMg, LiMg,and NaMg) complexes

New kinds of sodium bonding complexes XH?···?NaH (X?=?HBe, LiBe, NaBe, HMg, LiMg, and NaMg) have been predicted and characterized in the present paper. For each XH?···?NaH complex, the hydride-sodium bond is formed between the negatively charged H atom of XH and the positively charged Na atom of NaH. Due to the formation of the complexes, both the X–H and the Na–H bonds are elongated, and the Na–H stretching vibrational frequency is redshifted. The interaction energies in the XH?···?NaH complexes at the MP2/6-311++G(3df, 3pd) level increased in the order: HBeH?···?NaH (?4.50?kcal/mol)?相似文献