On the accurate measurement of amide one-bond 15N-1H couplings in proteins: effects of cross-correlated relaxation, selective pulses and dynamic frequency shifts

Amide one-bond 15N-1H scalar couplings of 15N- and [15N,2H]-isotopically enriched ubiquitin have been measured with the Quantitative J approach by monitoring NMR signal intensity modulation. Scalar couplings of the non-deuterated protein are in average approximately 0.6 Hz larger than values of deuterated ubiquitin. This deviation is 30 times the error derived from experiment reproducibility. Refocusing dipole/dipole cross-correlated relaxation decreases the discrepancy to approximately 0.1 Hz, suggesting that it likely originates from relaxation interference. Alternatively, the subtraction of J values obtained at different magnetic fields largely reduces the relaxation effects. In contrast, the dynamic frequency shift whose main contribution to 1J(15N-1H) arises from 15N chemical shielding anisotropy/NH dipole cross-correlation, is not eliminated by refocusing spin evolution under this interaction. Furthermore, the average difference of 1J(15N-1H) values at two magnetic fields closely agrees with the theoretical expected difference in the dynamic frequency shift.     

Large-scale ultrasonic cleaning system: Design of a multi-transducer device for boat cleaning (20kHz)

The present study is part of a global project which consists in the development of an automatic cleaning station for immersed boats (cockle, ninepin, etc.) in a self-service mode, associating an innovative ultrasonic device for cleaning with a specific water treatment. The originality of the process is that cleaning is performed by three transducers operating simultaneously at low frequency and moving along the surface, thanks to programmable logic controllers, and that it includes a suction to collect the dirt removed. Therefore, the time required for boat maintenance is shortened, ensuring high quality cleaning without the need for dry docks and avoiding additional pollution in the harbor areas. One of the key points was the evaluation of washing efficiency, as it is really hard to give a quantitative estimation of the dirt removed. To obtain the first design laws, feasibility tests have been carried out on dirty cockle samples and on real boat hulls with a laboratory ultrasonic device. The influence of a large number of parameters was tested such as transducer-probe distance, displacement speed and transmitted power. The obtained data allowed us to design an optimized cleaning device combining high efficiency and speed.     

Simulating Dirac fermions with Abelian and non-Abelian gauge fields in optical lattices

In this work we present an optical lattice setup to realize a full Dirac Hamiltonian in 2+1 dimensions. We show how all possible external potentials coupled to the Dirac field can arise from perturbations of the existing couplings of the honeycomb lattice pattern. This greatly simplifies the proposed implementations, requiring only spatial modulations of the intensity of the laser beams to induce complex non-Abelian potentials. We finally suggest several experiments to observe the properties of the quantum field theory in the setup.     

Dimerization in the commensurate network of 4-n-octyl-4’-cyanobiphenyl (8CB) molecules adsorbed on MoS $_\mathsf{2}$ single crystal

By combining X-ray diffraction under grazing incidence (GIXD) and scanning tunneling microscopy (STM) measurements, we have determined the structure of 4-n-octyl-4-cyanobiphenyl (8CB) molecules adsorbed on MoS₂, under the thick organic film. The commensurability of the adsorbed network and the unit cell structure have been determined, revealing a complex 2D structure. This structure is characterized by straight ribbons with two types of ribbons, alternatively stacked. In one type, molecules are equally spaced, as they are paired in the other type. Considering the energetics of adsorption with a model of single ribbon, we recover the two observed ribbon structures. The alternate stacking of the ribbons appears as a consequence of the connection between the commensurabilities in the two main crystallographic directions. Moreover, we have found a particularly high value for the molecule-substrate potential corrugations, indicating that the dipole moment of 8CB molecules could play a fundamental role in the molecule-substrate interactions.Received: 1 April 2004, Published online: 29 June 2004PACS: 61.10.-i X-ray diffraction and scattering - 68.35.Bs Structure of clean surfaces (reconstruction) - 61.30.-v Liquid crystals - 68.35.Md Surface thermodynamics, surface energies     

Two Types of σ-Allenyl Complexes from Reactions of Silylenes and Germylenes with Chromium Fischer Alkynyl(alkoxy)carbenes

The reactivity of amidinatotetrylenes of the type E(tBu₂bzm)R¹ (E=Si, Ge; tBu₂bzm=N,N′-bis(tertbutyl)benzamidinate; R¹=alkyl or aryl) with the chromium Fischer alkynylcarbene complexes [Cr{C(OEt)C₂R²}(CO)₅] (R²=Ph; ferrocenyl, Fc) has been studied. At room temperature, two different reaction pathways have been identified: (a) attack of the amidinatotetrylene to the alkynyl C² atom (γ-attack), which leads to σ-allenyl complexes in which the original C_carbene atom maintains its attachment to the Cr(CO)₅ and OEt groups (compounds 3 ), and (b) attack of the amidinatotetrylene to the C_carbene atom (α-attack), which ends in σ-allenyl complexes in which the original C_carbene atom is not attached to the metal atom and has been inserted into an E−N bond of the amidinatotetrylene forming an E-C-N-C-N five-membered ring (compounds 4 ). It has been found that compounds 3 are thermodynamically less stable than their corresponding 4 isomers and that some of the former (E=Ge; R¹=CH₂SiMe₃) can be transformed into the latter upon heating. At high temperatures (>70 °C) the reactions involving bulky amidinatotetrylenes (R¹=Mes, tBu) end in the carbene-substitution products [Cr{E(tBu₂bzm)R¹}(CO)₅].     

A Mechanistically and Operationally Simple Route to Metal–N-Heterocyclic Carbene (NHC) Complexes

We have been puzzled by the involvement of weak organic and inorganic bases in the synthesis of metal–N-heterocyclic carbene (NHC) complexes. Such bases are insufficiently strong to permit the presumed required deprotonation of the azolium salt (the carbene precursor) prior to metal binding. Experimental and computational studies provide support for a base-assisted concerted process that does not require free NHC formation. The synthetic protocol was found applicable to a number of transition-metal- and main-group-centered NHC compounds and could become the synthetic route of choice to form M–NHC bonds.     

An Expedient Method for the Umpolung Coupling of Enols with Heteronucleophiles**

In this paper, we present an unprecedented and general umpolung protocol that allows the functionalization of silyl enol ethers and of 1,3-dicarbonyl compounds with a large range of heteroatom nucleophiles, including carboxylic acids, alcohols, primary and secondary amines, azide, thiols, and also anionic carbamates derived from CO₂. The scope of the reaction also extends to carbon-based nucleophiles. The reaction relies on the use of 1-bromo-3,3-dimethyl-1,3-dihydro-1λ³[d][1,2]iodaoxole, which provides a key α-brominated carbonyl intermediate. The reaction mechanism has been studied experimentally and by DFT, and we propose formation of an unusual enolonium intermediate with a halogen-bonded bromide.     

Rational Tuning of the Reactivity of Three-Membered Heterocycle Ring Openings via SN2 Reactions

The development of small-molecule covalent inhibitors and probes continuously pushes the rapidly evolving field of chemical biology forward. A key element in these molecular tool compounds is the “electrophilic trap” that allows a covalent linkage with the target enzyme. The reactivity of this entity needs to be well balanced to effectively trap the desired enzyme, while not being attacked by off-target nucleophiles. Here we investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with a nitrogen (aziridine), phosphorus (phosphirane), oxygen (epoxide) or sulfur atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring opening of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C₆H₁₀Y with Y=NH, PH, O, S). It was revealed that the activation energy of the ring opening does not necessarily follow the trend that is expected from C−Y leaving-group bond strength, but steeply decreases from Y=NH, to PH, to O, to S. We illustrate that the HOMO_Nu–LUMO_Substrate interaction is an all-important factor for the observed reactivity. In addition, we show that the activation energy of aziridines and phosphiranes can be tuned far below that of the corresponding epoxides and thiiranes by the addition of proper electron-withdrawing ring substituents. Our results provide mechanistic insights to rationally tune the reactivity of this class of popular electrophilic traps and can guide the experimental design of covalent inhibitors and probes for enzymatic activity.