Theoretical study of B3O radical isomers and their interconversion pathways

Despite the fact that B₃O is the second simplest B _n O radical after BO, a controversy recently emerged concerning the molecular structure of its global minimum. Two recent theoretical groups predicted the linear quartet BBBO to be the ground isomer. By contrast, another recent theoretical group reported that B₃O has a doublet B₃-ring ground structure. Moreover, larger B _n O clusters usually have low-lying B₃-ring isomers. In order to determine the accurate energetic competition between linear and cyclic structures in both the doublet and quartet, and to understand the detailed isomerism between various isomers, which is vital for understanding the formation mechanism of B₃O, we report the first potential energy surface (PES) study of B₃O at various computational levels, including CCSD(T)/6-311+G(2df), CCSD(T)/aug-cc-pVTZ, CCSD(T)/aug-cc-pVQZ and G3B3 for the single-point energy, as well as B3LYP/6-311+G(d) and QCISD/6-311+G(d) for geometrical optimisation. It is shown that the isomers in the quartet state are all thermodynamically more stable than the corresponding doublet ones, and on both the quartet and doublet PESs, the linear form has the lowest energy. Therefore, our study on both linear and cyclic isomers shows that the linear quartet BBBO ⁴ 01 is definitively the ground isomer. Although being much less stable than the quartet linear BBBO global minimum by >20 kcal mol^?1, five cyclic isomers exist as local minima, with the bi-cyclic structure ⁴ 02 possessing the smallest barrier of around 15 kcal mol^?1. The dissociation energies for direct combination processes B₃ + O, B₂ + BO and B + B₂O are discussed. The present work may be helpful in obtaining a deep understanding of the doping and oxidation process of pure B _n clusters.     

Infrared spectroscopy of closed s-shell gas-phase M+(N2O)n (M = Li,Al) ion-molecule complexes*

ABSTRACT

We present the results of a combined experimental and computational study of the structures of gas-phase M⁺(N₂O)_n (M?=?Li, Al) complexes. Infrared spectra were recorded in the region of the N₂O asymmetric (N?=?N) stretch using photodissociation spectroscopy employing the inert messenger technique. Unlike in our previous studies on M⁺(N₂O)_n (M?=?Cu, Ag, Au and M?=?Co, Rh, Ir) complexes, N– and O–bound isomers in this case are near isoenergetic and are not distinguished spectroscopically at this resolution. In the case of Li⁺ complexes, there is, however, evidence for the presence of bound N₂ moieties, indicating the presence of inserted, OLi⁺N₂(N₂O)_n–type structures. The weak N₂ band lies to the blue of the signature of molecularly N– and O–bound ligands and is well–reproduced in the simulated spectra of energetically low-lying structures computed from density functional theory. No such inserted isomers are observed in the case of Al⁺(N₂O)_n complexes whose infrared spectra can be understood on the basis of molecularly-bound N₂O ligands. The differences in M⁺(N₂O)_n structures observed for these closed–shell, ns², metal centres relative to other metal cations are discussed in terms of the likely bonding motifs.     

Structural Assignment of Stilbenethiols and Chalconethiols and Differentiation of Their Isomeric Derivatives by Means of 1H‐ and 13C‐NMR Spectroscopy

Abstract

The ¹H‐ and ¹³C‐NMR spectra of some substituted stilbenes and chalcones were assigned unambiguously on the basis of a combination of homo‐ (COSY) and heteronuclear (HETCOR) two‐dimensional methods, the chemical shifts, as well as spin‐coupling constants. The A_ik empirical parameters of the –O–C(S)–N(CH₃)₂, –S–C(O)–N(CH₃)₂, and –SH group were calculated to help predict the chemical shifts of substituted stilbenes, 4′‐nitrostilbenes, and chalcones. The ¹H‐ and ¹³C‐NMR spectra have been shown to be able to differentiate between the isomers of O‐stilbenyl (4, 5) and S‐stilbenyl N,N‐dimethylthiocarbamates (7, 8) as well as O‐chalconyl (6) and S‐chalconyl N,N‐dimethylthiocarbamates (9).     

Structures,vibrational spectra,and relative energetics of FC(O)ONO and FC(O)NO2 isomers at DFT and ab initio levels

The structural and vibrational parameters of FC(O)ONO and FC(O)NO₂ isomers were examined theoretically using the B3LYP/6-311+G(3df) and CCSD(T)/6-311G(d) methods. Four conformers of FC(O)ONO isomer and one FC(O)NO₂ isomer are found here. Among them, the trans–cis and cis–cis FC(O)ONO configuration are new conformers. The energetics were refined with G3//B3LYP and CBS-QB3 calculations. The trans–trans conformer of the FC(O)ONO isomer is found to be the lowest energy structure, with an estimated heat of formation of ?104.9 kcal mol^?1 at 0 K as determined from CBS-QB3 theory. The next lowest structure is the cis–trans FC(O)ONO lying 1.7 kcal mol^?1 above the trans–trans structural form. The highest energy structure is the FC(O)NO₂ isomer with a predicted heat of formation of ?84.8 kcal mol^?1. A comparison of the relative stability of the FCNO₃ isomers with the isomers of ClCNO₃ shows that the Cl analogues follow the same pattern of stability, as do the F isomers. However, the chlorine isomers are unstable relative to their fluorine analogues.     

Two Mn(II) and Zn(II) Coordination Polymers: Aqueous-Phase Detection of Nitroaromatic Explosives and Protective Effect on Atherosclerosis

Via the solvothermal reaction between Zn(II) or Mn(II) salts and 5-(3,4-dicarboxylphenoxy)nicotinic acid (H₃L) ligand, a trifunctional N,O-building block having three diverse kinds of functional groups (O-ether, N-pyridyl and COOH), two new coordination polymers (CPs) could be generated, and their chemical formulae respectively are {[Mn₃(L)₂(H₂O)₂]·4H₂O} (1) and {[Zn(HL)]·NMP} (2). The complex 2 based on Zn(II) possesses high efficiency of fluorescence quenching for the nitrophenol (2,4,6-trinitrophenol, TNP; 4-nitrophenol, 4-NP; 3-nitrophenol, 3-NP; 2-nitrophenol, 2-NP) in the aqueous solution. Furthermore, the treatment activity of compounds on the atherosclerosis was assessed, and relevant mechanism was investigated. First of all, the ELISA assay was used to measure the content of the inflammatory cytokines released into the plasma. Besides, the levels of the NF-κb signaling pathway in the vascular endothelial cells were measured with real time RT-PCR. The hemolysis test was conducted in this research to measure the biocompatibility of the new compound.

     

(H2O)6的稳定结构及异构过程研究

(H₂O)₆是形成三维立体结构的最小水分子团簇并具有能量较低的多个稳定异构体.本文利用从头计算方法研究了各稳定结构的异构化过程.(H₂O)₆的环状结构与最稳定结构的能量差0.31 eV为一个氢键的键能.水分子团簇的异构化是分子间氢键打开或重组的过程,不同异构体之间的转化每次只涉及一个氢键的打开或重组,异构化的能垒高度在0.07—0.21 eV之间. 关键词： 水分子团簇 2O)₆')" href="#">(H₂O)₆ 异构化过程 从头计算     

Isotope effect of hydrated clusters of hydrogen chloride,HCl(H2O) n and DCl(H2O) n (n = 0–4): application of dynamic extended molecular orbital method

The recently proposed dynamic extended molecular orbital (DEMO) method is applied to the HCl(H₂O) _n and DCl(H₂O) _n (n = 0–4) clusters in order to explore the isotope effect on their structures, wavefunctions, and energies, theoretically. Since the DEMO method determines both electronic and nuclear wavefunctions simultaneously by optimizing all parameters including basis sets and their centres variationally, we can get the different nuclear orbitals for proton and deuteron as well as their electronic wavefunctions. The positions of the centres of nuclear orbitals show that the deuteron has weaker hydrogen bonding than the proton. There are three isomers in the case of n = 3 clusters, and less stable isomers have hydrogen transferred and non-transferred structures. In the conventional MO calculation, both hydrogen transferred and non-transferred isomers are calculated to be energy minima. When we have applied the DEMO method, only the hydrogen transferred structure is obtained for HCl(H₂O)₃, while both structures are optimized for DCl(H₂O)₃. Such strong H/D dependence on the structures of the HCl(H₂O) _n and DCl(H₂O) _n clusters can be expressed directly by using the DEMO method. The present application demonstrates that the DEMO method is a useful tool for analysing the anharmonicity and vibronic effects of a hydrogen bonding system.     

Pressure-induced phase transitions in gypsum

Abstract

We report high-pressure Raman scattering spectroscopy and energy dispersive X-ray diffraction investigations on gypsum, CaSO₄ · 2H₂O, at room temperature in a diamond cell. With increasing pressure, measurements indicate that CaSO₄ · 2H₂O undergoes two stages of crystalline-state phase transitions at 5 and 9 GPa, and then converts to a disordered phase above 11 GPa. The structures of the three high-pressure phases of gypsum have not been determined yet. These phases are tentatively named as “post-gypsum-I” (PG-I), “post-gypsum-II” (PG-II) and “disordered” according to the sequence of their appearance with pressure.

Gypsum shows anisotropic compressibility along three crystallographic axes with b > c > a below 5 GPa. The difference in the behavior of the two OH stretching modes in gypsum is attributed to the different reduction rate in the hydrogen bonding distances by the anisotropic axial compressibility.     

Theoretical study of the [Si,C, P,O] potential energy surface

The structures, energetics, spectroscopies and stability of the doublet [Si, C, P, O] radical are explored at the density functional theory and ab initio levels. Eighteen isomers connected by 22 interconversion transition states are located at the DFT/B3LYP/6-311G(d) level. The structures of the kinetically stable isomers and the relevant transition states are further optimized at the QCISD/6-311G(d) level followed by CCSD(T)/6-311 + G(2df) single-point energy calculations. At the QCISD/6-311G(d) level, the lowest-lying isomer is the cyclic O-cCSiP 8 (0.0 kcal/mol) with considerable kinetic stability of 22.0 kcal/mol. In addition, two bent isomers OSiCP 1 (7.3 kcal/mol) and SiCPO 3 (34.7 kcal/mol) also possess considerable kinetic stability (more than 10.0 kcal/mol). As a result, three isomers 1, 3 and 8 are predicted to be possible candidates for future experimental and astrophysical detection. The bonding nature of the three isomers is analysed. The calculated results are compared with those of the analogous radical [Si, C, N, O]. Implications in the laboratory and interstellar space are also discussed. The predicted structures and spectroscopic properties are expected to be informative for the identification of [Si, C, P, O] in the laboratory and space.     

SPECTROSCOPIC PROPERTIES AND ELECTRONIC STRUCTURE OF [CuCl(L-PROLINATO)(H2O)]

ABSTRACT

[CuCl(L-Prolinato)(H₂O)] was prepared. Its electronic absorption spectrum and photoacoustic spectrum were recorded at the room temperature. A semi-empirical method of ligand-field-theory PLFT was utilized to calculate the d-d transition energy. According to the results, the spectrum was explained satisfactorily.     

Optical absorption studies on cobalt doped struvite

Abstract

Optical absorption spectrum of cobalt doped MgNH₄PO₄ · 6H₂O (struvite) is investigated in UV-VIS-NIR regions. The spectrum in UV-VIS-NIR region is attributed to Co²⁺ in octahedral symmetry whereas the IR spectrum is attributed to vibrations due to PO₄ ^3-, NH₄ ⁺ and H₂O. The following crystal field (Dq) and interelectronic repulsion (B, C) parameters are evaluated: Dq = 940cm^?1, B = 870cm^?1 and C = 3970cm^?1.     

Conversion of ortho-para H2O isomers in water and a jump in erythrocyte fluidity through a microcapillary at a temperature of 36.6±0.3°C

A mechanism is proposed for the previously observed [1] jump in erythrocyte fluidity through a microcapillary 1.3 μm in diameter at a temperature of 36.6±0.3°C. Our interpretation is based on the experimental evidence both for existence of ortho and para H₂O isomers in water and on spin-selective interaction of proteins with para H₂O isomers as hydration shells of biomolecules are being formed [2]. It is important that the formation of hydration shells of proteins and DNA in aqueous solutions is accompanied by an increase in the Brillouin shift to 0.4 cm⁻1 (≃0.25 cm⁻¹ in water), which points to the formation of icelike structures. We believe that the coincidence of the translational energy kT of the Brownian motion and the energy of the rotational quanta for the 3₁₃–2₀₂ transition of para H₂O isomers at the temperature 36.6°C increases the probability for excitation of para H₂O isomers in collisions. Collisions mix quantum states of closely spaced levels in para H₂O (3₁₃, 285.2 cm⁻¹) and ortho H₂O (3₃₀, 285.4 cm⁻¹) and induce conversion of para isomers to ortho H₂O. It is assumed that this conversion in the icelike hydration shell of hemoglobin (Hb) is accelerated under the catalyzing effect of oxygen and iron present in Hb and triggers a chain reaction: release of ortho H₂O isomers through the erythrocyte membrane→compaction of Hb molecules and increase in concentration of catalysts→acceleration of conversion→structural gel-sol transition. It is the sequence of these processes that provides a jump in fluidity of erythrocytes through a microcapillary and the anomalous increase in fluidity of the aqueous solution of hemoglobin by almost an order of magnitude at temperatures close to 36.6°C and an increase in the solution concentration by a factor of 1.7.     

Calculation on the CO2 influences on the structure,stability of (MgO)m (m = 1–6) clusters

ABSTRACT

The concentration of carbon dioxide (CO₂) has a significant influence on the morphology of thermal decomposition products of magnesite. So, structures, stabilities and adsorption mechanisms of (MgO)_m (m?=?1–6) clusters by one or two CO₂ molecules were calculated by the GGA-PW91 method. The results show that the stability of the considered clusters is (MgO)_m(CO₂)₂ clusters > (MgO)_m(CO₂) clusters > (MgO)_m clusters by the average binding energy. Certain low-lying isomers of (MgO)_m(CO₂) and (MgO)_m(CO₂)₂ clusters which have an isolated O atom are deviating from the cluster center which possess higher kinetic activity. (MgO)_m clusters prefer to adsorb a CO₂ molecule, while (MgO)₃(CO₂) clusters prefer to adsorb a CO₂ molecule rather than the neighbors. Magnesite is difficult to transit to (MgCO₃)₂ clusters at room temperature. However, magnesite will spontaneously transit to (MgO)₂ clusters and further transit to MgO crystal which need to adsorb more energy at 700?K.     

Determination of Intracellular Carbonic Anhydrase Activity and Bicarbonate Permeability in Intact Colon Epithelia by Observation of the 18O-labelling of Co2

Abstract

We applied a mass spectrometric method, developed by Itada and Forster [1] for erythrocyte suspensions, which observes the exchange of ¹⁸O between HCO₃ ^?, CO₂ and H₂O, to determine intracellular carbonic anhydrase activity, A _i , and bicarbonate permeability, P, in intact guinea pig colon epithelium. To study the validity of the results with intact distal and proximal colon epithelia, we compared them with measurements of A_i and P in suspensions of isolated epithelial cells from the distal and proximal guinea pig colon. In both parts of the colon there is good agreement between the A_i values of colonocytes in suspension and in the intact colon epithelium. In addition we tested the temperature dependence of A_i and P, the oxygen supply to the colon during the measurements, and the intactness of the epithelial cells by trypan blue staining. We conclude that it is valid to use the method of Itada and Forster [1] with intact colon epithelial sheets.

This new application allows us to study separately the apical and serosal membrane of the epithelial cells. We used the method to determine whether there is a short chain fatty acid – bicarbonate exchanger in the apical or serosal membrane of proximal and distal colon epithelium. For this purpose we measured the membrane bicarbonate permeability in the presence and absence of 25 mM propionate in the reaction solution. Only in the apical membrane of the proximal colon we find a higher P in presence of propionate than in its absence, showing that there the transport of short chain fatty acids is coupled to that of bicarbonate.     

The HO4H → O3 + H2O reaction catalysed by acidic,neutral and basic catalysts in the troposphere

A detailed effects of catalyst X (X?=?H₂O, (H₂O)₂, NH₃, NH₃···H₂O, H₂O···NH₃, HCOOH and H₂SO₄) on the HO₄H → O₃?+?H₂O reaction have been investigated by using quantum chemical calculations and canonical vibrational transition state theory with small curvature tunnelling. The calculated results show that (H₂O)₂-catalysed reactions much faster than H₂O-catalysed one because of the former bimolecular rate constant larger by 2.6–25.9 times than that of the latter one. In addition, the basic H₂O···NH₃ catalyst was found to be a better than the neutral catalyst of (H₂O)₂. However it is marginally less efficient than the acidic catalysts of HCOOH, and H₂SO₄. The effective rate constant (k'_t) in the presence of catalyst X have been assessed. It was found from k'_t that H₂O (at 100% RH) completely dominates over all other catalysts within the temperature range of 280–320?K at 0?km altitude. However, compared with the rate constant of HO₄H → H₂O?+?O₃ reaction, the k _eff values for H₂O catalysed reaction are smaller by 1–2 orders of magnitude, indicating that the catalytic effect of H₂O makes a negligible contribution to the gas phase reaction of HO₄H → O₃?+?H₂O.

Highlights

• A detailed effects of catalyst of H₂O, (H₂O)₂, NH₃, NH₃···H₂O, H₂O···NH₃, HCOOH and H₂SO₄ on the HO₄H → O₃?+?H₂O reaction has been performed.

• From energetic viewpoint, H₂SO₄ exerts the strongest catalytic role in HO₄H → O₃?+?H₂O reaction as compared with the other catalysts.

• At 0 km altitude H₂O (at 100% RH) completely dominates over all other catalysts within the temperature range of 280–320 K.

• HO₄H → H₂O?+?O₃ reaction with H₂O cannot be compete with the reaction without catalyst, due to the fact that the effective rate constants in the presence of H₂O are smaller.

     

Theoretical investigation on structures,stability and properties of [P,X, Y] (X=C,Si; Y = O,S) isomers

The structures, energetics and stability of the [P, X, Y] (X?=?C, Si; Y?=?O, S) radicals are explored by means of the density functional theory and ab initio levels. Seventeen [P, X, Y] isomers and 14 interconversion transition states are obtained at the B3LYP/6-311G(d) level. At the CCSD(T)/6-311?+?G(2df)//QCISD/6-311G(d)?+?ZPVE level, the lowest-lying isomers are the linear PCO 1a (0.0?kcal/mol), PCS 1b (0.0) and the three-membered ring cPSiO 1c (0.0), cPSiS 1d (0.0) on their respective potential energy surfaces. These four isomers exhibit considerably not only thermodynamic but also kinetic stabilities. Additionally, the cyclic cPCS 2b (32.8) and linear PSiS 2d (18.6) possess also high kinetic stability. All of six isomers 1a, 1b, 2b, 1c, 1d and 2d are considerably stabilized by a barrier of at least 20?kcal/mol, and may be detected in the laboratory or interstellar space. Their valence bond structures and possible formation strategies in the laboratory and space are discussed in detail. Finally, the similarities and discrepancies on structures and stabilities between [P, X, Y] (X?=?C, Si; Y?=?O, S) isomers are compared. These predicted results are highly expected to be informative for the future identification of [P, X, Y] (X?=?C, Si; Y?=?O, S) in the laboratory and space.     

Tree species of the central amazon and soil moisture alter stable isotope composition of nitrogen and oxygen in nitrous oxide evolved from soil

The use of stable isotopes of N and O in N₂O has been proposed as a way to better constrain the global budget of atmospheric N₂O and to better understand the relative contributions of the main microbial processes (nitrification and denitrification) responsible for N₂O formation in soil. This study compared the isotopic composition of N₂O emitted from soils under different tree species in the Brazilian Amazon. We also compared the effect of tree species with that of soil moisture, as we expected the latter to be the main factor regulating the proportion of nitrifier- and denitrifier-derived N₂O and, consequently, isotopic signatures of N₂O. Tree species significantly affected δ ¹⁵N in nitrous oxide. However, there was no evidence that the observed variation in δ ¹⁵N in N₂O was determined by varying proportions of nitrifier- vs. denitrifier-derived N₂O. We submit that the large variation in δ ¹⁵N-N₂O is the result of competition between denitrifying and immobilizing microorganisms for NO 3 m . In addition to altering δ ¹⁵N-N₂O, tree species affected net rates of N₂O emission from soil in laboratory incubations. These results suggest that tree species contribute to the large isotopic variation in N₂O observed in a range tropical forest soils. We found that soil water affects both ¹⁵N and ¹⁸O in N₂O, with wetter soils leading to more depleted N₂O in both ¹⁵N and ¹⁸O. This is likely caused by a shift in biological processes for ¹⁵N and possible direct exchange of ¹⁸O between H₂O and N₂O.     

Theory of chemical bonds in metalloenzymes XX: magneto-structural correlations in the CaMn4O5 cluster in oxygen-evolving complex of photosystem II

ABSTRACT

Magneto-structural correlations in oxygen-evolving complex (OEC) of photosystem II (PSII) have been elucidated on the basis of theoretical and computational results in combination with available electron paramagnetic resonance (EPR) experimental results, and extended x-ray absorption fine structure (EXAFS) and x-ray diffraction (XRD) results. To this end, the computational methods based on broken-symmetry (BS) UB3LYP solutions have been developed to elucidate magnetic interactions in the active manganese catalyst for water oxidation by sunlight. The effective exchange interactions J for the CaMn(III)Mn(IV)₃O₅(H₂O)₃Y(Y = H₂O or OH^?) cluster (1) model of OEC of PSII have been calculated by the generalised approximate spin projection (GAP) method that eliminates the spin contamination errors of the BS UB3LYP solution. Full geometry optimisations followed by the zero-point energy (ZPE) correction have been performed for all the spin configurations of 1 to improve the J values that are compared with accumulated EPR in the S₂ state of Kok cycle and magnetic susceptibility results of Christou model complex Ca₂Mn(IV)₃O₄ (2). Using the calculated J values, exact diagonalisation of the spin Hamiltonian matrix has been carried out to obtain excitation energies and spin densities of the ground and lower excited states of 1. The calculated excitation energies are consistent with the available experimental results. The calculated spin densities (projection factors) are also compatible with those of the EPR results. The calculated spin densities have been used to calculate the isotropic hyperfine (A_iso) constants of ⁵⁵Mn ions revealed by the EPR experiments. Implications of the computational results are discussed in relation to the structural symmetry breaking (SSB) in the S₁, S₂ and S₃ states, spin crossover phenomenon induced by the near-infrared excitation and the right- and left-handed scenarios for the O–O bond formation for water oxidation.     

ESR spectroscopics study of radicals formed from methoxycarbonylcholine picrate hemihydrate

Abstract

The electron spin resonance of γ-irradiated single crystals of methoxycarbonylcholine picrate hemihydrate, C₇H₁₆NO₃ ⁺ · C₆H₂N₃O₇ ^? · ½ H₂O has been observed and analyzed for different orientations of the crystal in the magnetic field. The crystals have been investigated between 70 and 350 K. The spectra were found to be temperature independent and the radiation damage centers are attributed to – ?[Obar]OCH₃ and –CH₂CH₂O? radicals. The g and hyperfine coupling constants were found to be almost isotropic with an average, g = 2.0060, a _H1 = 4.4G for –CH₂CH₂O?, g = 2.0050, a _H2 = 3.5G for –CH₂CH₂O? and g = 2.0045, a _H = 3.5 G for –?[Obar]OCH₃. These values indicate a long-range coupling between the unpaired electron and H protons.     

Characterisation of geometric isomers of europium chlorides with 2,2′-bipyridine based on X-ray diffraction,luminescence and quantum chemical data

A low-temperature high-resolution luminescence study of the EuCl₃bpy₂(H₂O) _n isomers has been carried out. The Eu³⁺ luminescence spectra of all geometric isomers were recorded over the spectral range which includes transitions from the ⁵D₀ excited state to the ⁷F_0–4 ground state manifolds and from the ⁵D₁ excited state to the ⁷F_0–2 ground state manifolds. Analysis of the Eu³⁺ transitions observed in the luminescence spectra shows that the Eu³⁺ ion occupies a spectroscopic site symmetry that approaches a C_{2 v} symmetry with distortion towards C₂ or lower symmetry. The structural features and distortions of the Eu³⁺ coordination polyhedron in these geometric isomers were described based on the X-ray crystallographic data as well. The splitting patterns and energies found of the ⁷F_0–4 manifolds have been used to calculate the crystal field parameters (CFPs) of the Eu³⁺ ions in these geometric isomers. In addition the mutual influence of the ligands as well as the relative stability of geometric isomers of the [EuCl₃bpy₂(H₂O)₂]⁺ cation in the gas phase was analyzed within DFT calculations.