Theoretical study of the H + HCN → H + HNC process

We present a theoretical study on the detailed mechanism and kinetics of the H+HCN →H+HNC process. The potential energy surface was calculated at the complete basis set quantum chemical method, CBS-QB3. The vibrational frequencies and geometries for four isomers (H₂CN, cis-HCNH, trans-HCNH, CNH₂), and seven saddle points (TSn where n = 1 ? 7) are very important and must be considered during the process of formation of the HNC in the reaction were calculated at the B3LYP/6-311G(2d,d,p) level, within CBS-QB3 method. Three different pathways (PW1, PW2, and PW3) were analyzed and the results from the potential energy surface calculations were used to solve the master equation. The results were employed to calculate the thermal rate constant and pathways branching ratio of the title reaction over the temperature range of 300 up to 3000 K. The rate constants for reaction H + HCN → H + HNC were fitted by the modified Arrhenius expressions. Our calculations indicate that the formation of the HNC preferentially occurs via formation of cis–HCNH, the fitted expression is k _{P W2}(T) = 9.98 × 10^?22 T ^2.41 exp(?7.62 kcal.mol^?1/R T) while the predicted overall rate constant k _{O v e r a l l} (T) = 9.45 × 10^?21 T ^2.15 exp(?8.56 kcal.mol^?1/R T) in cm ³ molecule ^?1 s ^?1.

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Graphical Abstract (a) Potential energy surface, (b) thermal rate constants as a function of temperature and (c) the branching ratios (%) of PW1, PW2, PW3 pathways involved in rm H + HCN → H + HNC process.

     

MQ-HCN-based pulse sequences for the measurement of 13C1′-1H1′, 13C1′-15N, 1H1′-15N, 13C1′-13C2′, 1H1′-13C2′, 13C6/8-1H6/8, 13C6/8-15N, 1H6/8-15N, 13C6-13C5, 1H6-13C5 dipolar couplings in 13C, 15N-labeled DNA (and RNA)

A suite of multiple quantum (MQ) HCN-based pulse sequences has been developed for the purpose of collecting dipolar coupling data in labeled nucleic acids. All the pulse sequences are based on the robust MQ-HCN experiment which has been utilized for assignment purposes in labeled nucleic acids for a number of years and provides much-needed resolution for the dipolar coupling measurements. We have attempted to collect multiple couplings centered on the 13C1' and 13C6/8 positions. Six pulse sequences are described, one each for measurement of one-bond 13C1'-1H1' and 13C6/8-1H6/8 couplings, one for measurement of one-bond 13C1'-15N and two-bond 1H1'-15N couplings, one for measurement of one-bond 13C6/8-15N and two-bond 1H6/8-15N couplings, one for measurement of one-bond 13C1'- 13C2' and two-bond 1H1'-13C2' couplings, and one for measurement of one-bond 13C6-13C5 and two-bond 1H6-13C5 couplings in the bases of C and T. These sequences are demonstrated for a labeled 18 bp DNA duplex in a 47 kDa ternary complex of DNA, CBFbeta, and the CBFalpha Runt domain, thus clearly demonstrating the robustness of the pulse sequences even for a very large complex.     

Conformational Peculiarities of Polynucleotides with a Nonrandom Base Sequence According to the 1H→ 3H Exchange Rate in C8H Groups of Purinic Residues

Abstract

We have determined the ¹H→³H exchange rate constants between water and C8H groups of purinic residues of alternating polynucleotides poly(dA-dT)·poly(dA-dT), poly(dG-dC)·poly(dG- dC) and poly(dA-dC)·poly(dG-dT) as well as homopolynucleotides poly(dA)·poly(dT) and poly(dG)·poly(dC) in aqueous solutions with high-salt concentrations (3 M NaCl and 4–6 M CsF), in water-ethanol (60%) solution and in 0.15 M NaCl at 25°C. The rate constants for adenine (k_A) and guanine (k_G) of polynucleotides were compared with corresponding constants for E.coli DNA, dGMP nd dAMP at the same conditions. The relation between exchange rates and conformations of polynucleotides permits the study of their conformational peculiarities in solution.

Of three alternating polynucleotides examined in 0.15 M NaCl the exchange retardation was observed only for poly(dA-dT)·poly(dA-dT) as compared with that in B-DNA, which is in good agreement with the B-alternating “wrinkled” DNA model. The conformations of poly(dG-dC)·poly(dG-dC) and poly(dA-dC)·poly(dG-dT), according to the exchange data obtained, are within the B form. For homopolynucleotides in 0.15 M NaCl, the k_A value for poly(dA)·poly(dT) is nearly the same as k_A for B-DNA, which indicates the similarity of their conformations, whereas the k_G value for poly(dG)·poly(dC) is 1.7-fold lower in comparison with the k_G value in B-DNA. This seems to be connected with the existence of B? A conformation equilibrium for poly(dG)·poly(dC) in solution.

The increase of NaCl concentration to 3 M results in a B→Z transition in the case of poly(dG-dC)·poly(dG-dC) and in the shift of B?A equilibrium towards the A-form in the case of poly(dG)·poly(dC), as is evidenced by alterations of their K_G values. Poly(dA-dT)·poly(dA-dT) in 6 M CsF and poly(dA-dC)·poly(dG-dT) in 4.3 M CsF maintain their inherent conformations in 0.15 M NaCl in spite of the fact that they are characterised by the “X-type” CD-spectrum at these conditions. According to the exchange data the conformation of poly(dA)·poly(dT) in 6 M CsF corresponds to the “heteronomous” DNA model or some other structure with lower accessibility of C8H groups of adenylic residues.     

Planar π-aromatic C3h B6H 3 + and π-antiaromatic C2h B8H2: boron hydride analogues of D3h C3H 3 + and D2h C4H4

Based upon extensive density functional theory and wave function theory calculations performed in this work, we predict the existence of the perfectly planar triangle C(3h) B(6)H(3)(+) (1, (1)A') and the double-chain stripe C(2h) B(8)H(2) (9, (1)A(g)) which are the ground states of the systems and the inorganic analogues of cyclopropene cation D(3h) C(3)H (3) (+) and cyclobutadiene D(2h) C(4)H(4), respectively. Detailed adaptive natural density partitioning (AdNDP) analyses indicate that C(3h) B(6)H (3) (+) is π plus σ doubly aromatic with two delocalized π-electrons and six delocalized σ-electrons formally conforming to the 4n + 2 aromatic rule, while C(2h) B(8)H(2) is π antiaromatic and σ aromatic with four delocalized π-electrons and ten delocalized σ-electrons. The perfectly planar C(2h) B(8)H(4) (5, (1)A(g)) also proves to be π antiaromatic analogous to D(2h) C(4)H(4), but it appears to be a local minimum about 50 kJ mol(-1) less stable than the three dimensional C(s) B(8)H(4)(6, (1)A'). AdNDP, nucleus independent chemical shifts (NICS) and electron localization function (ELF) analyses indicate that these boron hydride clusters form islands of both σ- and π-aromaticities and are overall aromatic in nature in ELF aromatic criteria.     

Iridium(I) dimers with bridging N,N′-di-p-tolylformamidine. X-ray molecular structure of Ir2(μ-p-CH3C6H4NCHN-p-C6H4CH3)(μ-NH-p-C6H4CH3)(C8H14)2

The reaction of [IrCl(COD)]₂ with K[CH(N-p- C₆H₄CH₃)₂] (K⁺form⁻) has been carried out in both neat toluene and in the presence of Bu^tOH. In the first case [Ir(form)(COD)]₂ (1) was obtained in good yields. The other reaction follows a somewhat different course with partial alcoholysis of the formamidine ligand and formation of Ir₂(μ-form)(μ-NH-p-C₆H₄CH₃)(COD)₂ (2). Crystal data for compound 2: space group P2₁/c, a = 9.389(2), b = 21.083(4), c = 16.810(2) Å, β = 91.54(1)° V=3326(2) ų, Z = 4, R = 0.0343 for 3707 data with F_o² > 3σ(F_o²).     

Synthetic Studies on Nephritogenic Glycosides. Synthesis of β-Glc-(1→6)-α-Glc-(l→6)-α-Glc-(1→Asn)

Gibberellins (GAs) A₉, A₁₅, A₁₉, A₂₀, A₂₉, A₃₅, A₄₄, A₅₀ and A₆₁ were identified by capillary gas chromatography/selected ion monitoring (GC/SIM) in immature seeds of loquat (Eriobotrya japonica Lindl). Furthermore, five unknown GA-like compounds with apparent parent ions of m/z 418, 504 or 506 (as methyl ester trimethylsilyl ether derivatives) were found by GC/mass spectrometry (GC/MS) in the biologically active fractions. The m/z 418 and 504 compounds may have been C-11β hydroxylated GA₉ and dehydro-GA₃₅, respectively. The bioassay and GC/MS results suggest that the major GAs were GA₅₀ and the five unknown GA-like compounds. In the immature seeds, at least two GA metabolic pathways may thus exist, one being the non-hydroxylation pathway of GA₁₅→GA₂₄→GA₉, and the other, the early C-13 hydroxylation pathway of GA₄₄→GA₁₉→GA₂₀→GA₂₉. A late C-11β hydroxylation pathway is also possible.     

H5N1禽流感病毒对C57BL／6小鼠的致病性研究

本试验利用虎源H5N1禽流感病毒对6～8周龄雌性C57BL/6小鼠进行滴鼻感染,观测小鼠临床症状和组织病理变化,于感染后第3d和第5d每组分别处死3只小鼠,测定肺、脑、脾、肾、肝组织中的病毒含量;并测定该病毒对C57BL/6小鼠的MLD50。结果表明感染小鼠出现精神不振、体重下降、支气管炎和间质性肺炎为主的临床症状和病理变化;测得感染后小鼠肺脏中病毒拷贝数和病毒滴度最高,其次是脑、肾、脾、肝等组织;该病毒对C57BL/6小鼠的MLD50为10-6.5/0.05mL。此研究成功进行了H5N1禽流感病毒对C57BL/6小鼠的感染,可以作为感染模型进行H5N1禽流感病毒的发病机制、疫苗评价、药物筛选等研究。     

Structural and electronic properties of Z isomers of (4α→6´´,2α→O→1´´)-phenylflavans substituted with R = H, OH and OCH₃ calculated in aqueous solution with PCM solvation model

In the search for new antioxidants, flavan structures called our attention, as substructures of many important natural compounds, including catechins (flavan-3-ols), simple and dimeric proanthocyanidins, and condensed tannins. In this work the conformational space of the Z-isomers of (4α→6′′, 2α→O→1′′)-phenylflavans substituted with R = H, OH and OCH₃ was scanned in aqueous solution, simulating the solvent by the polarizable continuum model (PCM). Geometry optimizations were performed at B3LYP/6-31 G** level. Electronic distributions were analyzed at a better calculation level, thus improving the basis set (6-311++G**). A topological study based on Bader′s theory (atoms in molecules) and natural bond orbital (NBO) framework was performed. Furthermore, molecular electrostatic potential maps (MEPs) were obtained and thoroughly analyzed. The stereochemistry was discussed, and the effect of the solvent was addressed. Moreover, intrinsic properties were identified, focusing on factors that may be related to their antioxidant properties. Hyperconjugative and inductive effects were described. The coordinated NBO/AIM analysis allowed us to rationalize the changes of MEPs in a polar solvent. To investigate the molecular and structural properties of these compounds in biological media, the polarizabilities and dipolar moments were predicted which were further used to enlighten stability and reactivity properties. All conformers were taken into account. Relevant stereoelectronic aspects were described for understanding the stabilization and antioxidant function of these structures.     

Density functional calculations for a high energy density compound of formula C6H6?n (NO2) n

A series of polynitroprismanes, C(6)H(6-n )(NO(2))(n) (n?=?1-6) intended for use as high energy density compounds (HEDCs) were designed computationally. Their electronic structures, heats of formation, interactions between nitro groups, specific enthalpies of combustion, bond dissociation energies, and explosive performances (detonation velocities and detonation pressures) were calculated using density functional theory (DFT) with the 6-311 G** basis set. The results showed that all of the polynitroprismanes had high positive heats of formation that increased with the number of substitutions for the prismane derivatives, while the specific enthalpy of combustion decreased as the number of nitro groups increased. In addition, the range of enthalpy of combustion reducing is getting smaller. Interactions between ortho (vicinal) groups deviate from the group additivity rule and decrease as the number of nitro groups increases. In terms of thermodynamic stability, all of the polynitroprismanes had higher bond dissociation energies (BDEs) than RDX and HMX. Detonation velocities and detonation pressures were estimated using modified Kamlet-Jacobs equations based on the heat of detonation (Q) and the theoretical density of the molecule (ρ). It was found that ρ, D, and P are strongly linearly related to the number of nitro groups. Taking both their energetic properties and thermal stabilities into account, pentanitroprismane and hexanitroprismane are potential candidate HEDCs.     

A B3LYP and MP2(full) theoretical investigation into the cooperativity effect between dihydrogen-bonding and H–M∙∙∙π (M = Li, Na, K) interactions among HF, MH with the π-electron donor C2H2, C2H4 or C6H6

The DFT-B3LYP/6-311++G(3df,2p) and MP2(full)/6-311++G(3df,2p) calculations were carried out on the binary complex formed by HM (M?=?Li, Na, K) and HF or the π-electron donor (C₂H₂, C₂H₄, C₆H₆), as well as the ternary system FH???HM???C₂H₂/C₂H₄/C₆H₆. The cooperativity effect between the dihydrogen-bonding and H–M???π interactions was investigated. The result shows that the equilibrium distances R _H???H and R _M???π in the ternary complex decrease and both the H???H and H–M???π interactions are strengthened when compared to the corresponding binary complex. The cooperativity effect of the dihydrogen bond on the H–M???π interaction is more pronounced than that of the M???π bond on the H???H interaction. Furthermore, the values of cooperativity effect follow the order of FH???HNa???π?>?FH???HLi???π?>?FH???HK???π and FH???HM???C₆H₆?>?FH???HM???C₂H₄?>?FH???HM???C₂H₂. The nature of the cooperativity effect was revealed by the analyses of the charge of the hydrogen atoms in H???H moiety, atom in molecule (AIM) and electron density shifts methods.

An endo-(1→6-β-D-glucanase from Mucor hiemalis

An endo-(1→6)-β-D-glucanase (EC 3.2.1), isolated from the culture filtrate of Mucor hiemalis, was purified by ammonium sulphate fractionation and gel filtration. The homogeneity of the enzyme was confirmed by disc electrophoresis. The enzyme had a wide range of temperature and pH stability, high substrate specificity, and an action pattern of the endo-type.     

北京地区随机人群C6、C7多态性研究

补体第六、七成分（C6、C7）具有遗传多态性。本文研究了北京地区随机人群115人的C6及137人的C7多态性分布,共检出C6等位基因有C6^*A、B、B2、M91、M1等5种。其中C6^*A和B为常见型。多态性共4种,即C7^*1、2、3、4,其中C7^*1为常见型。     

Enzymic synthesis of O-β-d-glucopyranosyl-(1→6)-d-galactose

1. The enzymic synthesis of O-β-d-glucopyranosyl-(1→6)-d-galactose has been described and evidence for the structure presented. 2. It has been shown that the transglycosylase of A. niger provides a convenient means of synthesizing (1→6)-linked disaccharides.     

The structure and properties of tetrakis(tironato)cerate(IV), Na12[Ce(C6H2O2(SO3)2)4]·9H2O·6C3H7NO

The title complex, prepared in 1 M NaOH, was crystallized from hot N,N-dimethylformamide/ ethanol solutions to give Na₁₂[Ce(C₆H₂O₂(SO₃)₂)₄]· 9H₂O·6DMF. The purple—brown crystals were examined by X-ray diffraction while inside quartz capillaries filled with DMF, (λ_max 425 nm, ϵ 3664; λ_sh 520 nm, ϵ 2240) and belong to space group Pbca, Z=8 with a=21.846(4), b=17.348(2), c=43.103- (6) Å, V=16.335(7) ų, D_c=1.693 gcm^t−3, D_o=1.725 g cm^t−3. Diffractometer data were collected using Mo Kα radiation to 2θ=43^o. For 7331 independent data with F_o²>3σ(F_o²) full matrix least squares refinement converged to unweighted and weighted R factors of 0.072 and 0.110, respectively, with a mixture of anisotropic and isotropic thermal parameters. The disordered DMF atom parameters were not refined. The structure consists of discrete monomeric Ce(C₆H₂S₂O₈)₄¹²⁻ units with 12 Na⁺ counter cations and 10 H₂O molecules (two with half occupancy), and 6 DMF molecules of solvation filling up spaces between cations and anions. Cerium(IV) is in a general position with a coordination polyhedron close to the trigonal-faced dodecahedron, D_2d, with the angles between the two BAAB trapezoids of 2.3^o and 3.7^o. The average CeO(A) distance, 2.363(9) Å is longer than the average CeO(B) distance, 2.326(15)Å, with the reverse being true for one of the four tironato ligands. The average ring OCeO angle is 67.9(1)^o. The cerium (IV) complex is found by cyclic voltammetry to undergo a quasi-reversible one-electron reduction (in strongly basic solution with excess tiron) with Ef=−497 mV vs. SCE, hence the ratio of the formation constants for tetrakis(tironato)cerate(IV) to that for tetrakis(tironato)cerate(III), K_IV/K_III, is 10³³. Characterization of other tiron salts is reported.     

The gene encoding vasoactive intestinal peptide is located on human chromosome 6p21→6qter

Summary Vasoactive intestinal peptide (VIP) is a regulatory neuropeptide involved in a wide variety of functions, among them vasodilation, smooth muscle relaxation, sweat secretion, gastrointestinal peristalsis, and pancreatic function. A deficient VIP-innervation of sweat glands was recently described as a possible pathogenic factor in sweating of cystic fibrosis (CF) patients. To investigate a possible role for a defective VIP-gene in cystic fibrosis, we have used a panel of rodent-human hybrid cells, retaining defined complements of human chromosomes to localize the VIP-gene to the human chromosome region 6p216qter. As the CF gene was recently mapped to chromosome 7, we conclude that the VIP-gene is not the primary gene defect in this disease.     

TheX → Y → Z scheme after 23 years

Mathematical modelling of the course of the immune response is undoubtedly one of the most progressive and most promising areas of modern immunology. Mathematical models (along with computer programs) can be taken as "the only means of thoroughly testing and examining a large and intricate theory" (Partridge et al. 1984). The first phase of construction of mathematical models is the formulation of assumptions based on the knowledge of the facts to be modelled (manifested usually in a scheme of the presumed course of the modelled process). The first mathematical models of immune response were based on the hypothesis of a two-stage differentiation of cells participating in the humoral response, published in Prague 23 years ago (Sercarz and Coons 1962; Sterzl 1962) and illustrated by the X----Y----Z scheme. Many contemporary mathematical models still stem from this scheme which undoubtedly fits the fundamental data concerning the immune system.     

Measurement of 1H�C15N and 1H�C13C residual dipolar couplings in nucleic acids from TROSY intensities

Analogous to the recently introduced ARTSY method for measurement of one-bond (1)H-(15)N residual dipolar couplings (RDCs) in large perdeuterated proteins, we introduce methods for measurement of base (13)C-(1)H and (15)N-(1)H RDCs in protonated nucleic acids. Measurements are based on quantitative analysis of intensities in (1)H-(15)N and (13)C-(1)H TROSY-HSQC spectra, and are illustrated for a 71-nucleotide adenine riboswitch. Results compare favorably with those of conventional frequency-based measurements in terms of completeness and convenience of use. The ARTSY method derives the size of the coupling from the ratio of intensities observed in two TROSY-HSQC spectra recorded with different dephasing delays, thereby minimizing potential resonance overlap problems. Precision of the RDC measurements is limited by the signal-to-noise ratio, S/N, achievable in the 2D TROSY-HSQC reference spectrum, and is approximately given by 30/(S/N) Hz for (15)N-(1)H and 65/(S/N) Hz for (13)C-(1)H. The signal-to-noise ratio of both (1)H-(15)N and (1)H-(13)C spectra greatly benefits when water magnetization during the experiments is not perturbed, such that rapid magnetization transfer from bulk water to the nucleic acid, mediated by rapid amino and hydroxyl hydrogen exchange coupled with (1)H-(1)H NOE transfer, allows for fast repetition of the experiment. RDCs in the mutated helix 1 of the riboswitch are compatible with nucleotide-specifically modeled, idealized A-form geometry and a static orientation relative to the helix 2/3 pair, which differs by ca 6° relative to the X-ray structure of the native riboswitch.