Characterization of the Simplest Thiolimine: The Higher Energy Tautomer of Thioformamide

As sulfur-containing organic molecules thioamides and their isomers are conceivable intermediates in prebiotic chemistry, for example, in the formation of amino acids and thiazoles and resemble viable candidates for detection in interstellar media. Here, we report the characterization of parent thioformamide in the solid state via single-crystal X-ray diffraction and its photochemical interconversion to its hitherto unreported higher energy tautomer thiolimine in inert argon and dinitrogen matrices. Upon photogeneration, four conformers of thiolimine form, whose ratio depends on the employed wavelength. One of these conformers interconverts due to quantum mechanical tunneling with a half-life of 30–45 min in both matrix materials at 3 and 20 K. A spontaneous reverse reaction from thiolimine to thioformamide is not observed. To support our experimental findings, we explored the potential energy surface of the system at the AE-CCSD(T)/aug-cc-pCVTZ level of theory and computed tunneling half-lives with the CVT/SCT approach applying DFT methods.     

基于磁共振的胞浆中无标记酵母细胞色素c构象变化追踪

细胞色素c(cytochrome c,cyt c)是一个重要的多功能蛋白.在线粒体中,它作为载体传递电子.而在细胞质中,它可能会作为凋亡起始因子启动细胞凋亡程序.复杂的细胞质环境是否会对其构象产生影响,以及产生怎样的影响,目前仍然没有得到确证.本研究通过无标记的基于甲基的核磁共振（nuclear magnetic resonance,NMR）技术追踪了野生型酿酒酵母iso-1 cyt c在酵母细胞匀浆液中的构象变化.发现cyt c在细胞匀浆中至少存在4种不同的氧化态构象和1种还原态构象.而且随着时间的推进,不同构象之间发生转换.结果表明cyt c的构象会随环境改变,这可能与抵抗氧化应激相关.     

Boron Tunneling in the “Weak” Bond-Stretch Isomerization of N−B Lewis Adducts

Some nitrile-boron halide adducts exhibit a double-well potential energy surface with two distinct minima: a “long bond” geometry (LB, a van der Waals interaction mostly based on electrostatics, but including a residual charge transfer component) and a “short bond” structure (SB, a covalent dative bond). This behavior can be considered as a “weak” form of bond stretch isomerism. Our computations reveal that complexes RCN−BX₃ (R=CH₃, FCH₂, BrCH₂, and X=Cl, Br) exhibit a fast interconversion from LB to SB geometries even close to the absolute zero thanks to a boron atom tunneling mechanism. The computed half-lives of the meta-stable LB compounds vary between minutes to nanoseconds at cryogenic conditions. Accordingly, we predict that the long bond structures are practically impossible to isolate or characterize, which agrees with previous matrix-isolation experiments.     

Essential dynamics for the study of microstructures in liquids

Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic‐molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen‐bonded clusters. © 2014 Wiley Periodicals, Inc.     

Size of a polymer chain in an environment of quenched chains

We perform high‐coordination three‐dimensional (3D) lattice simulations of a single chain of N monomers embedded in matrices of quenched chains, at different concentrations ρ, using pruned‐enriched Rosenbluth sampling. The partition function is well‐described by the expression, , where is a universal constant, and is the concentration dependent lattice connectivity constant. For sufficiently long chains, , we find that the radius of gyration R varies nonmonotonically with ρ; R decreases gradually from its unperturbed dimensions R₀ until , after which it increases relatively rapidly due to repulsion between monomers. Motivated by the similarity in the shape of the curves, and results on Gaussian chains, we successfully superpose all the simulation data onto a single master curve. Finally, we test the relationship , suggested by a Flory‐type scaling model, where ρ_c is the critical percolation threshold, and is a universal constant. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1611–1619     

Amino Acid Chirality and Ferrocene Conformation Guided Self‐Assembly and Gelation of Ferrocene–Peptide Conjugates

The self‐assembly and gelation behavior of a series of mono‐ and disubstituted ferrocene (Fc)–peptide conjugates as a function of ferrocene conformation and amino acid chirality are described. The results reveal that ferrocene–peptide conjugates self‐assemble into organogels by controlling the conformation of the central ferrocene core, through inter‐ versus intramolecular hydrogen bonding in the attached peptide chain(s). The chirality controlled assembling studies showed that two monosubstituted Fc conjugates FcCO–L FL FL A‐OMe and FcCO–L FL FD A‐OMe form gels with nanofibrillar network structures, whereas the other two diastereomers FcCO–D FL FL A‐OMe and FcCO–L FD FL A‐OMe exclusively produced straight nanorods and non‐interconnected small fibers, respectively. This suggests the potential tuning of gelation behavior and nanoscale morphology by altering the chirality of constituted amino acids. The current study confirms the profound effect of diastereomerism and no influence of enantiomers on gelation. Correspondingly, the diastereomeric and enantiomeric Fc[CO‐FFA‐OMe]₂ were constructed for the study of chirality‐organized structures.     

Conformational Plasticity in Glycomimetics: Fluorocarbamethyl‐L‐idopyranosides Mimic the Intrinsic Dynamic Behaviour of Natural Idose Rings

Sugar function, structure and dynamics are intricately correlated. Ring flexibility is intrinsically related to biological activity; actually plasticity in L ‐iduronic rings modulates their interactions with biological receptors. However, the access to the experimental values of the energy barriers and free‐energy difference for conformer interconversion in water solution has been elusive. Here, a new generation of fluorine‐containing glycomimetics is presented. We have applied a combination of organic synthesis, NMR spectroscopy and computational methods to investigate the conformational behaviour of idose‐ and glucose‐like rings. We have used low‐temperature NMR spectroscopic experiments to slow down the conformational exchange of the idose‐like rings. Under these conditions, the exchange rate becomes slow in the ¹⁹F NMR spectroscopic chemical shift timescale and allows shedding light on the thermodynamic and kinetic features of the equilibrium. Despite the minimal structural differences between these compounds, a remarkable difference in their dynamic behaviour indeed occurs. The importance of introducing fluorine atoms in these sugars mimics is also highlighted. Only the use of ¹⁹F NMR spectroscopic experiments has permitted the unveiling of key features of the conformational equilibrium that would have otherwise remained unobserved.     

Stabilization of zwitterionic proline by DMSO

Zwitterionic stabilization and metal‐free organocatalysis are two emerging topics. In this work, the numbers of DMSO molecules required to render zwitterionic proline geometrically stable, energetically preferential, and conformationally predominant have been determined, as one, three, and three, respectively. Conformations are analyzed for proline conformers interacted with one, two, and three DMSO molecules, and three DMSO molecules are enough to fill up the first shell of proline. Relative stabilities of two selected canonical structures are dependent on the DMSO contents, while zwitterionic stabilities improve monotonously with increase of DMSO contents. DMSO causes a conformational diversity and good zwitterionic stabilization effects, which result from the synergetic effects of two types of H‐bonding interactions. With increase of DMSO contents, type‐2 H‐bonding (CH as donors) contributes more to zwitterionic stabilization. At any DMSO content, zwitterionic proline is facile to form because of low activation energies, and this study helps to understand proline‐catalyzed processes. © 2015 Wiley Periodicals, Inc.     

Simulation Study on the Coil‐Globule Transition and Surface Adsorption of HP Chains

The coil‐globule transition of short hydrophobic‐polar (HP) chains, composed of 24 hydrophilic monomers and 24 polar monomers, in solution and on hydrophobic surface and the adsorption of the HP chain on hydrophobic surface are simulated. The coil‐globule transition point of the HP chain is dependent on sequence of chain but is roughly independent of the surface adsorption strength. Whereas the critical adsorption point of the HP chain is roughly independent of sequence. In addition, the lowest energy states can be obtained for the HP chain in solution or on surface by Monte Carlo simulated annealing method. Results show that the statistical conformation is strongly dependent on the intrachain H‐H attraction strength and the surface adsorption strength.

     

A Sharp Thermal Transition of Fast Aromatic‐Ring Dynamics in Ubiquitin

Aromatic amino acid side chains have a rich role within proteins and are often central to their structure and function. Suitable isotopic‐labelling strategies enable studies of sub‐nanosecond aromatic‐ring dynamics using solution NMR relaxation methods. Surprisingly, it was found that the three aromatic side chains in human ubiquitin show a sharp thermal dynamical transition at approximately 312 K. Hydrostatic pressure has little effect on the low‐temperature behavior, but somewhat decreases the amplitude of motion in the high‐temperature regime. Therefore, below the transition temperature, ring motion is largely librational. Above this temperature, a complete ring‐rotation process that is fully consistent with a continuous diffusion not requiring the transient creation of a large activated free volume occurs. Molecular dynamics simulations qualitatively corroborate this view and reinforce the notion that the dynamical character of the protein interior has much more liquid‐alkane‐like properties than previously appreciated.