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     

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.     

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.     

NMR Spectroscopic Analysis Reveals Extensive Binding Interactions of Complex Xyloglucan Oligosaccharides with the Cellvibrio japonicus Glycoside Hydrolase Family 31 α‐Xylosidase

The study of the interaction of glycoside hydrolases with their substrates is fundamental to diverse applications in medicine, food and feed production, and biomass‐resource utilization. Recent molecular modeling of the α‐xylosidase CjXyl31A from the soil saprophyte Cellvibrio japonicus, together with protein crystallography and enzyme‐kinetic analysis, has suggested that an appended PA14 protein domain, unique among glycoside hydrolase family 31 members, may confer specificity for large oligosaccharide fragments of the ubiquitous plant polysaccharide xyloglucan (J. Larsbrink, A. Izumi, F. M. Ibatullin, A. Nakhai, H. J. Gilbert, G. J. Davies, H. Brumer, Biochem. J. 2011 , 436, 567–580). In the present study, a combination of NMR spectroscopic techniques, including saturation transfer difference (STD) and transfer NOE (TR‐NOE) spectroscopy, was used to reveal extensive interactions between CjXyl31A active‐site variants and xyloglucan hexa‐ and heptasaccharides. The data specifically indicate that the enzyme recognizes the entire cello‐tetraosyl backbone of the substrate and product in positive enzyme subsites and makes further significant interactions with internal pendant α‐(1→6)‐linked xylosyl units. As such, the present analysis provides an important rationalization of previous kinetic data on CjXyl31A and unique insight into the role of the PA14 domain, which was not otherwise obtainable by protein crystallography.     

Enantioselective Organocatalytic Addition of Oxazolones to 1,1‐Bis(phenylsulfonyl)ethylene: A Convenient Asymmetric Synthesis of Quaternary α‐Amino Acids

A new, easy, and highly enantioselective method for the synthesis of quaternary α‐alkyl‐α‐amino acids based on organocatalysis is reported. The addition of oxazolones to 1,1‐bis(phenylsulfonyl)ethylene is efficiently catalyzed by simple chiral bases or thioureas. The reaction affords α,α‐disubstituted α‐amino acid derivatives with complete C4 regioselectivity and with excellent yields and enantioselectivities. This methodology is complementary to previously reported enantioselective approaches to quaternary α‐amino acids and allows the synthesis of α‐phenyl‐α‐alkyl‐α‐amino acids and α‐tert‐butyl‐α‐alkyl‐α‐amino acids. It has distinct advantages in terms of operational simplicity, enviromentally friendly conditions, and suitability for large‐scale reactions.     

Chemical basis of peptidoglycan discrimination by PrkC, a key kinase involved in bacterial resuscitation from dormancy

Bacterial Ser/Thr kinases modulate a wide number of cellular processes. In Bacillus subtilis , the Ser/Thr kinase PrkC has been shown to induce germination of bacterial spores in response to DAP-type but not Lys-type cell wall muropeptides. Muropeptides are a clear molecular signal that growing conditions are promising, since they are produced during cell wall peptidoglycan remodeling associated with cell growth and division of neighboring bacteria. However, whether muropeptides are able to bind the protein physically and how the extracellular region is able to distinguish the two types of muropeptides remains unclear. Here we tackled the important question of how the extracellular region of PrkC (EC-PrkC) senses muropeptides. By coupling NMR techniques and protein mutagenesis, we exploited the structural requirements necessary for recognition and binding and proved that muropeptides physically bind to EC-PrkC through DAP-moiety-mediated interactions with an arginine residue, Arg500, belonging to the protein C-terminal PASTA domain. Notably, mutation of this arginine completely suppresses muropeptide binding. Our data provide the first molecular clues into the mechanism of sensing of muropeptides by PrkC.