pH‐controlled reaction divergence of decarboxylation versus fragmentation in reactions of dihydroxyfumarate with glyoxylate and formaldehyde: parallels to biological pathways

The reactions of dihydroxyfumarate with glyoxylate and formaldehyde exhibit a unique pH‐controlled mechanistic divergence leading to different product suites by two distinct pathways. The divergent reactions proceed via a central intermediate (2,3‐dihydroxy‐oxalosuccinate, 3 , in the reaction with glyoxylate and 2‐hydroxy‐2‐hydroxymethyl‐3‐oxosuccinate, 14 , in the reaction with formaldehyde). At pH 7–8, products ( 7 , 8 , and 15 ) exclusively from a decarboxylation of the intermediate are observed, while at pH 13–14, products ( 9 , 10 , and 16 ) solely derived from a hydroxide‐promoted fragmentation of the intermediate are formed. The decarboxylative and fragmentation pathways are mutually exclusive and do not appear to coexist under the range of pH (7–14) conditions investigated. Herein, we employ a combination of quantitative ¹³C NMR measurements and density functional theory calculations to provide a rationale for this pH‐driven reaction divergence. These rationalizations also hold true for the reactions of dihydroxyfumarate produced in situ by the catalytic cyanide‐mediated dimerization of glyoxylate. In addition, the non‐enzymatic decarboxylation and fragmentation transformations of these central intermediates ( 3 and 14 ) appear to have intriguing parallels to the enzymatic reactions of oxalosuccinate and formation of glyceric acid derivatives in extant metabolism – the high and low pH mimicking the precise control exerted by the enzymes over reaction pathways. Copyright © 2016 John Wiley & Sons, Ltd.     

Reactions of chlorination with tert‐butyl hypochlorite (TBuOCl)

The chlorination reactions of nitrogenous organic compounds (2,2,2‐trifluoroethylamine, benzylamine, glycine, and dimethylamine) by tert‐butyl hypochlorite (^tBuOCl) were studied at 25 °C, ionic strength 0.5 M and under isolation conditions. The kinetic results obtained in the formation processes of the corresponding N‐chloramines in acid medium (pH = 5–7) are summarized in this paper. Kinetic studies showed a first order with respect to ^tBuOCl concentration. The chlorination reactions involving benzylamine, glycine and dimethylamine were all first order with respect to nitrogenous compound concentration and approximately ?1 order with respect to proton concentration. The reaction with 2,2,2‐trifluoroethylamine was more complex, and the order of reaction with respect to the amine varied with pH. Copyright © 2014 John Wiley & Sons, Ltd.     

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.     

Selective Correlation of Amide Groups to Glycine Alpha Protons and of Arginine Guanidine Groups to Delta Protons in Proteins by Multiple Quantum Spectroscopy

A new 3D pulse sequence correlates backbone amide proton and nitrogen with alpha proton resonances selectively for glycine residues in a fully doubly labeled (¹⁵N,¹³C) protein. The excitation of multiple quantum coherences provides optimized resolution and sensitivity. Degenerate alpha proton groups can be promptly recognized. Correlation of guanidine NH groups to delta protons of arginine side chains is also obtained.     

Use of N‐chloro‐N‐methyl‐p‐toluenesulfonamide in N‐chlorination reactions

Second‐order rate constants (k₂) were determined for the addition of ten nitrogenous organic compounds (benzylamine, 2,2,2‐trifluoethylamine chlorhidrate, methylamine chlorhidrate, glycine ethyl ester chlorhidrate, glycine, glycylglycine chlorhidrate, morpholine, pyperidine, pyperazine and dimethylamine) to the N‐chloro‐N‐methyl‐p‐toluenesulfonamide (NCNMPT) in the formation reaction of N‐chloramines in aqueous solution at 25 °C and ionic strength 0.5 M. The series of nucleophiles considered is structurally very varied and covers five pK_a units. The kinetic behaviour is similar for all compounds, being the elementary step the transfer of chlorine from the NCNMPT molecule to the nitrogen of the free amino group. These reactions were found first order in both reagents. The values of the rate constants indicate that the more basic amines produce N‐chloramines more readily. Rate constants for the nucleophilic attack are shown to correlate with literature data for some of these nitrogenous organic compounds in their reaction with N‐methyl‐N‐nitroso‐p‐toluenesulfonamide. Both reactions involve that the rate determining step is the attack of nitrogenous compounds upon electrophilic centre (Cl or else NO group). NCNMPT is a particularly interesting substrate, for which has not hitherto been published kinetic information, that allows us to assess the efficiency and the competitiveness of this reaction and compare it with other agents with a Cl⁺ atom. Copyright © 2013 John Wiley & Sons, Ltd.     

Anilinolysis of O‐butyl phenyl phosphonochloridothioate in acetonitrile: Synthesis,characterization, kinetic study,and reaction mechanism

This paper describes a simple optimized method for the synthesis of O‐butyl phenyl phosphonochloridothioate ( 4 ) under mild conditions. The target compounds were characterized by ¹H‐nuclear magnetic resonance (NMR), ¹³C‐NMR, and ³¹P‐NMR spectroscopy, as well as mass spectroscopy. The apparent structure of 4 was confirmed by optimization using the B3LYP/6‐311 + G(d,p) level in the Gaussian 09 program in acetonitrile. The nucleophilic substitution reactions of 4 with X‐anilines (XC₆H₄NH₂) and deuterated X‐anilines (XC₆H₄ND₂) were investigated kinetically in acetonitrile at 55.0°C. The free energy relationship with X in the anilines looked biphasic concave upwards with a break region between X = H and X = 3‐MeO, giving large negative ρ_X and small positive β_X values. The deuterium kinetic isotope effects were secondary inverse (k_H/k_D < 1: 0.789‐0.995) and the magnitudes, (k_H/k_D), increased when the nucleophiles were changed from weakly basic to strongly basic anilines. A concerted S_N2 mechanism is proposed on the basis of the selectivity parameters and the variation trend of the deuterium kinetic isotope effects with X.     

13C Nuclear Magnetic Resonance Studies of the Conformations of Serine‐3′‐ and 5′‐Thymidine Monophosphate Conjugates

The differences in the backbone conformation between O‐thymidine‐3′‐(1) and 5′‐yl O‐alkyl N‐phosphoryl serine methyl esters (2) have been investigated by solution ¹³C NMR spectroscopy. The stereo‐sensitive vicinal ³¹P–¹³C coupling constants were measured and used in the conformational analysis for the P–O5′–C5′, P–O3′–C3′, and P–N–C_α bonds. Three‐dimensional structural characteristics of dephosphorylation reactions of Compounds are also discussed.     

9Be + 12C, 9Be + 16O,9Be + 19F reactions at energies below the barrier

The ¹⁶O + ⁹Be reactions have been studied from E_c.m. = 2.0 MeV to 5.1 MeV, an energy near the top of the Coulomb barrier. The cross section for the neutron transfer reaction ⁹Be(¹⁶O,¹⁷O¹ (0.87 MeV))⁸Be has been measured over this range by detecting the prompt 0.87 MeV γ-rays. The total fusion cross section has been determined from E_c.m. = 2.8 to 5.1 MeV by observing individual γ-ray transitions in the evaporation residues with a Ge(Li) detector, and then summing the separate yields. Direct processes are found to dominate the reaction yield below E_c.m. = 4 MeV. A comparison of the energy dependence of the fusion cross section for this reaction and the ¹²C + ¹³C reaction, which proceeds via the formation of the same compound nucleus, ²⁵Mg, reveals differences at sub-barrier energies. Optical model and incoming-wave boundary condition calculations are presented. Data have also been obtained for the near optimum Q-value neutron-transfer reactions ⁹Be(¹²C, ¹³C¹)⁸Be and ⁹Be(¹⁹F, ²⁰F)⁸Be, and these are discussed in terms of a simple model of sub-barrier direct reactions.     

Search for cluster structure of excited states in 14 C

We have studied three different 2n-transfer reactions on a ¹²C target, the 2p pick-up reaction on ¹⁶O and the ⁵He transfer in the reaction ⁹Be(⁷Li,d)¹⁴C. Combined with a systematic search through experimental results for transfer reactions, inelastic excitations and other data, we have established an almost complete spectroscopy for ¹⁴C up to 18 MeV excitation. We identify states with single-particle structure that have oblate shapes and states corresponding to proton excitations that are connected to oblate (triangular) cluster states. Further we list states of prolate shape which have no simple structure related to the low-lying oblate states of ¹²C. These are proposed to have strong -clustering and to form rotational bands as a parity inversion doublet, with high moment of inertia. With these results it is possible for the first time to identify chain states expected in the isotope ¹⁴C.Received: 3 November 2003, Revised: 23 December 2003, Published online: 24 August 2004PACS: 21.10.-k Properties of nuclei; nuclear energy levels - 21.60.Gx Cluster models     

Adsorption and reaction of glycine on the rutile TiO2(011) single crystal surface

The adsorption and reaction of glycine on the surface of a rutile TiO₂(011) single crystal has been studied by X-ray Photoelectron Spectroscopy (XPS) and Temperature Programmed Desorption (TPD) techniques. Special attention was given to the formation and stability of the zwitterion structure (⁺NH₃–CH₂–COO^?) in comparison to that of the dissociated structure (NH₂–CH₂–COO^?). Both species have been observed on the surface at 300 K. The zwitterion structure was found less stable than the dissociated structure. This is in line with other experimental results related to proline on rutile TiO₂(110) single crystal [13, 14], glycine on rutile TiO₂(110) single crystal [17, 24] and computational results related to glycine on rutile TiO₂(110) single crystal [25]. By 500 K most of the zwitterion structure has been converted to the dissociated one. TPD results indicated that glycine reacts in a similar way to carboxylic acids on this surface with the main decomposition products being ketene (CH₂=C=O). Other masses left unassigned for were also observed during TPD. The most intense being m/e 55 that might be due to =CH–C(O)N=or C(O)N=CH fragments.     

Mass yield in high-energy proton-uranium collisions from a complete,microcanonical statistical decay

The properties of charge exchange reactions induced by¹³C projectiles of 30 MeV/u are discussed. Spectra on¹²C as target have been measured and are used to illustrate the properties of the (¹³C,¹³N) and (¹³C,¹³B) reactions. Both reactions show selective population of states, the (¹³C,¹³B) reactions favours the spin-flip (Δs=1) transitions.The Giant Dipole Resonance is strongly excited in both reactions.     

Substituent effect investigation of 3‐(2, 4‐dichlorophenyl)‐1‐(4′‐X‐phenyl)‐2‐propen‐1‐one. Part 1. Correlation analysis of 13C NMR chemical shifts

A series of substituted chlorinated chalcones namely, 3‐(2,4‐dichlorophenyl)‐1‐(4′‐X‐phenyl)‐2‐propen‐1‐one, have been synthesized, X being H, NH₂, OMe, Me, F, Cl, CO₂Et, CN, and NO₂. Dual substituent parameter (DSP) models of ¹³C NMR chemical shift (CS) have revealed that π‐polarization concept could be utilized to explain the reverse field effect at CO, the enhanced substituent field effect at CO, C‐2, and C‐5, and the decreased sensitivity of substituent field effect at C‐6. Chlorine atoms dipole direction at the benzylidene ring either enhances or reduces substituent effect depending on how they couple with the substituent dipole at the probe site. The correlation of ¹³C NMR CS of C‐2, C‐5, and C‐6 with σ and σ indicates that chlorine atoms in the benzylidine ring deplete the ring from charges. Both MSP of Hammett and DSP of Taft ¹³C NMR CS models give similar trends of substituent effects at C‐2, C‐5, and C‐6. However, the former fail to give a significant correlation for CO and C‐6 ¹³C NMR CS. MSP of σ_q and DSP of Taft and Reynolds models significantly correlated ¹³C NMR CS of C_β. MSP of σ_q fails to correlate C‐1′ ¹³C NMR CS. Investigation of ¹³C NMR CS of non‐chlorinated chalcones series: 3‐phenyl‐1‐(4′‐X‐phenyl)‐2‐propen‐1‐one has revealed similar trends of substituent effects as in the chlorinated chalcones series for C‐1′, CO, C_α, and C_β. In contrast, the substituent effect of the non‐chlorinated chalcone series at C‐2, C‐5, and C‐6 did not correlate with any substituent constant. Copyright © 2010 John Wiley & Sons, Ltd.     

Monitoring synchrotron X‐ray‐induced radiolysis effects on metal (Fe,W) ions in high‐temperature aqueous fluids

Radiolysis‐induced effects on aqueous tungsten ions are observed to form a precipitate within seconds upon exposure to a synchrotron X‐ray micro‐beam in a WO₃ + H₂O system at 873 K and 200 MPa. In situ Fe K‐edge energy‐dispersive X‐ray absorption spectroscopy (ED‐XAS) measurements were made on Fe(II)Cl₂ aqueous solutions to 773 K in order to study the kinetics of high‐temperature reactions of Fe²⁺ and Fe³⁺ ions with transient radiolysis species. The radiolytic reactions in a fluid sample within a hydrothermal diamond anvil cell result in oxidation of the Fe²⁺ ion at 573 K and reduction of Fe³⁺ at temperatures between 673 and 773 K and of the Fe²⁺ ion at 773 K. The edge‐energy drift evident in the ED‐XAS data directly reflects the kinetics of reactions resulting in oxidation and/or reduction of the Fe²⁺ and Fe³⁺ ions in the aqueous solutions at high temperatures. The oxidation and reduction trends are found to be highly consistent, making reliable determinations of reaction kinetics possible.     

Determination of Multiple φ-Torsion Angles in Proteins by Selective and Extensive C Labeling and Two-Dimensional Solid-State NMR

We describe an approach to efficiently determine the backbone conformation of solid proteins that utilizes selective and extensive ¹³C labeling in conjunction with two-dimensional magic-angle-spinning NMR. The selective ¹³C labeling approach aims to reduce line broadening and other multispin complications encountered in solid-state NMR of uniformly labeled proteins while still enhancing the sensitivity of NMR spectra. It is achieved by using specifically labeled glucose or glycerol as the sole carbon source in the protein expression medium. For amino acids synthesized in the linear part of the biosynthetic pathways, [1-¹³C]glucose preferentially labels the ends of the side chains, while [2-¹³C]glycerol labels the C^α of these residues. Amino acids produced from the citric-acid cycle are labeled in a more complex manner. Information on the secondary structure of such a labeled protein was obtained by measuring multiple backbone torsion angles φ simultaneously, using an isotropic–anisotropic 2D correlation technique, the HNCH experiment. Initial experiments for resonance assignment of a selectively ¹³C labeled protein were performed using ¹⁵N–¹³C 2D correlation spectroscopy. From the time dependence of the ¹⁵N–¹³C dipolar coherence transfer, both intraresidue and interresidue connectivities can be observed, thus yielding partial sequential assignment. We demonstrate the selective ¹³C labeling and these 2D NMR experiments on a 8.5-kDa model protein, ubiquitin. This isotope-edited NMR approach is expected to facilitate the structure determination of proteins in the solid state.     

Structure of neutron-rich Be and C isotopes

The structure of neutron-rich beryllium isotopes has been investigated using different heavy-ion-induced transfer reactions. In neutron transfer reactions, the population of final states shows a strong sensitivity to the chosen core nucleus, i.e., the target nuclei ⁹Be or ¹⁰Be, respectively. Molecular rotational bands up to high excitation energies are observed with ⁹Be as the core due to its pronounced 2α-cluster structure, whereas only a few states at low excitation energies are populated with ¹⁰Be as the core. For ¹¹Be, a detailed investigation has been performed for the three states at 3.41, 3.89, and 3.96 MeV, which resulted in the most probable spin-parity assignments 3/2⁺, 5/2^?, and 3/2^?, respectively. Furthermore, we have studied particle-hole states of ¹⁶C using the ¹³C(¹²C, ⁹C)¹⁶C reaction and found 14 previously unknown states. Using the ¹²C(¹²C, ⁹C)¹⁵C reaction, five new states were observed for ¹⁵C.     

Investigation of 91Zr by high resolution (d,p), (p,p′) and (p,d) reactions

Energy spectra and angular distributions of light particles (Z = 3–8) produced in the reactions ¹³C+^{58, 60, 64}Ni have been measured at 105 MeV. Coincidence events between light outgoing particles Li, Be, B and α, p have been observed for the first time in the ¹³C+⁵⁸Ni and ¹³C+⁶⁴Ni reactions. The results show that at least part of the ‘deep-inelastic’ events are due to many-particle reactions.     

Palladium‐catalyzed cyclization of 2‐alkynyl‐N‐ethanoyl anilines to indoles: synthesis,structural, spectroscopic,and mechanistic study

This study reports a facial regio‐selective synthesis of 2‐alkyl‐N‐ethanoyl indoles from substituted‐N‐ethanoyl anilines employing palladium (II) chloride, which acts as a cyclization catalyst. The mechanistic trait of palladium‐based cyclization is also explored by employing density functional theory. In a two‐step mechanism, the palladium, which attaches to the ethylene carbons, promotes the proton transfer and cyclization. The gas‐phase barrier height of the first transition state is 37 kcal/mol, indicating the rate‐determining step of this reaction. Incorporating acetonitrile through the solvation model on density solvation model reduces the barrier height to 31 kcal/mol. In the presence of solvent, the electron‐releasing (–CH₃) group has a greater influence on the reduction of the barrier height compared with the electron‐withdrawing group (–Cl). These results further confirm that solvent plays an important role on palladium‐catalyzed proton transfer and cyclization. For unveiling structural, spectroscopic, and photophysical properties, experimental and computational studies are also performed. Thermodynamic analysis discloses that these reactions are exothermic. The highest occupied molecular orbital?lowest unoccupied molecular orbital gap (4.9–5.0 eV) confirms that these compounds are more chemically reactive than indole. The calculated UV–Vis spectra by time‐dependent density functional theory exhibit strong peaks at 290, 246, and 232 nm, in good agreement with the experimental results. Moreover, experimental and computed ¹H and ¹³C NMR chemical shifts of the indole derivatives are well correlated. Copyright © 2015 John Wiley & Sons, Ltd.     

Hydrolytic reactions of cyclic bis(3′‐5′)diadenylic acid (c‐di‐AMP)

Hydrolytic reactions of cyclic bis(3′‐5′)diadenylic acid (c‐di‐AMP) have been followed by Reversed phase high performance liquid chromatography (RP‐HPLC) over a wide pH range at 90 °C. Under neutral and basic conditions (pH ≥ 7), disappearance of the starting material (first‐order in [OH^?]) was accompanied by formation of a mixture of adenosine 2′‐monophosphate and 3′‐monophosphate (2′‐AMP and 3′‐AMP). Under very acidic conditions (from H₀ = ?0.7 to 0.2), c‐di‐AMP undergoes two parallel reactions (first‐order in [H⁺]): the starting material is cleaved to 2′‐AMP and 3′‐AMP and depurinated to adenine (i.e., cleavage of the N‐glycosidic bond), the former reaction being slightly faster than the latter one. At pH 1–3, isomerization to cyclic bis(2′‐5′)diadenylic acid competes with the depurination. Copyright © 2012 John Wiley & Sons, Ltd.     

The (12C, 8Be) reaction on 12C, 16O, 24,26Mg, 40,48Ca, 54Fe AND 58Ni between 50 and 65 MeV bombarding energy

Absolute cross sections have been measured for the (¹²C, ⁸Be_g.s.) reaction from the target nuclei ¹²C, ¹⁶O, ²⁴Mg, ²⁶Mg, ⁴⁰Ca, ⁴⁸Ca, ⁵⁴Fe and ⁵⁸Ni at various energies between 50 and 65 MeV bombarding energy (lab) using a highly efficient detection system for ⁸Be. The results are presented in form of particle spectra and angular distributions. Except for the lightest target nuclei ¹²C and ¹⁶O, the cross sections decrease rapidly with angle and a one-step direct reaction mechanism is indicated. Satisfactory agreement of the data is obtained with DWBA calculations, using the finite range computer code LOLA of DeVries which treats recoil effects exactly. The spectroscopic factors extracted for the (¹²C, ⁸Be) reaction are close to those obtained from (⁶Li, d), (⁷Li, t) and (¹⁶O, ¹²C) reactions. The selective excitation of the same final states in all of these reactions, as far as data are available, and the close agreement of the spectroscopic factors are interpreted as evidence for a rather simple α-transfer in these reactions in contrast to a more complicated transfer of four nucleons.