Infrared and ab initio studies on 1,2,4,5-tetrafluorobenzene clusters with methanol and 2,2,2-trifluoroethanol: presence and absence of an aromatic C-H...O hydrogen bond

The (1:1) clusters of 1,2,4,5-tetrafluorobenzene (TFB) with methanol and with 2,2,2-trifluoroethanol (TFE) were studied both experimentally and computationally. Through use of fluorescence-detected infrared spectroscopy, the (1:1) clusters were identified in supersonic jets. Intermolecular interactions in the clusters were characterized by the spectral shifts of the aromatic C-H stretching modes in the TFB moiety owing to the cluster formation. The molecular structures, stabilization energies, and vibrational frequencies of the clusters were computed at the MP2/6-31+G level. Both computational and experimental data indicate that an aromatic C-H...O hydrogen bond is present in the TFB-methanol cluster, while it is absent in the TFB-TFE cluster.     

Photoreduction of polyhalogenated anthraquinones by direct electron transfer from alcohol

Polyhalogenated anthraquinones such as perfluoroanthraquinone, 1,2,3,4-tetrafluoroanthraquinone, and 1,2,3,4-tetrachloroanthraquinone are photoreduced in ethanol via direct electron transfer from ethanol. A dramatic switch-over from hydrogen-atom abstraction to electron transfer is induced by mixing ofππ with nπ^* states in their T₁ state and the enhanced electron-accepting character of polyhalogenated anthraquinones.     

Application of two-dimensional NMR spectroscopy to the complete analysis of the 1H and 13C NMR spectra of d-biotin in aqueous solution

The ¹H and ¹³C NMR spectra of d-biotin were observed at 400 and 100 MHz, respectively. Various types of two-dimensional NMR spectroscopy were performed to assign the spectra. The previous assignment of ¹³C NMR spectrum of d-biotin reported by Bradbury and Johnson was modified, and the dihedral angles between the C? H bonds of the ring were determined. The populations of the conformers produced by internal rotation around the C-2? C-δ bond were estimated.     

Electron–Proton Decoupling in Excited‐State Hydrogen Atom Transfer in the Gas Phase

Hydrogen‐release by photoexcitation, excited‐state‐hydrogen‐transfer (ESHT), is one of the important photochemical processes that occur in aromatic acids and is responsible for photoprotection of biomolecules. The mechanism is described by conversion of the initial state to a charge‐separated state along the O(N)‐H bond elongation, leading to dissociation. Thus ESHT is not a simple H‐atom transfer in which a proton and a 1s electron move together. Here we show that the electron‐transfer and the proton‐motion are decoupled in gas‐phase ESHT. We monitor electron and proton transfer independently by picosecond time‐resolved near‐infrared and infrared spectroscopy for isolated phenol–(ammonia)₅, a benchmark molecular cluster. Electron transfer from phenol to ammonia occurred in less than 3 picoseconds, while the overall H‐atom transfer took 15 picoseconds. The observed electron‐proton decoupling will allow for a deeper understanding and control of of photochemistry in biomolecules.     

Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement

KRAS homo-dimerization has been implicated in the activation of RAF kinases, however, the mechanism and structural basis remain elusive. We developed a system to study KRAS dimerization on nanodiscs using paramagnetic relaxation enhancement (PRE) NMR spectroscopy, and determined distinct structures of membrane-anchored KRAS dimers in the active GTP- and inactive GDP-loaded states. Both dimerize through an α4–α5 interface, but the relative orientation of the protomers and their contacts differ substantially. Dimerization of KRAS-GTP, stabilized by electrostatic interactions between R135 and E168, favors an orientation on the membrane that promotes accessibility of the effector-binding site. Remarkably, “cross”-dimerization between GTP- and GDP-bound KRAS molecules is unfavorable. These models provide a platform to elucidate the structural basis of RAF activation by RAS and to develop inhibitors that can disrupt the KRAS dimerization. The methodology is applicable to many other farnesylated small GTPases.     

A Tightly Stretched Ultralong Supramolecular Multiporphyrin Array Propagated by Double‐Strand Formation

A shape‐programmed linearity through supramolecular polymerization is demonstrated by a step‐growth double‐strand formation of a telechelic oligomeric porphyrin array in which two alternating pyridyl‐porphyrin sequenced units are held together by self‐complementary ligand‐to‐metal coordination. The stiff rod‐like structure and sufficiently large binding constant of the double‐strand unit considerably extended a supramolecular array in the one dimension, which produced a tightly stretched string with a length that exceeded several micrometers.     

A Palladium-mediated DNA Base Pair of a β-C-Nucleoside Possessing a 2-Aminophenol as the Nucleobase

Abstract

An approach we have used in this study for the incorporation of metal ions into DNA, is the direct modification of a DNA base itself, turning it into a metal-chelating nucleobase wherein two nucleobases are paired through metal coordination. Herein we report the X-ray crystal structure of a synthetic intermediate 6 for the aminophenol bearing nucleoside 3 and its metal coordination properties with Pd²⁺. The anomeric configuration of the nucleoside was unequivocally determined to be β-form by the X-ray analysis of 6; the structure has been resolved by direct methods (S1R97) and expanded using Fourier techniques (DIRDIF94) using 2628 independent reflections with I>2.00 [sgrave](I) and 425 parameters. Final R (R_w) was 0.037 (0.043): orthorhombic, space group P2₁2₁2₁ (#19) with a=16.562(1) Å, b=16.933(1) Å, c=11.205(1) Å, and V=3142.2(4) ų; D_c =1.369g/cm³ for Z=4, and molecular weight 647.65. This result is consistent with the tentative assignment by our previous ¹H NOE differentiation experiments. Detailed ¹H NMR studies showed that the nucleoside forms a stable 2:1 complex with Pd²⁺ with concomitant deprotonation of its phenolic proton. Although there are two possible structures (cis or trans) for the square-planar Pd²⁺ complex, the ratio of cis to trans was approximately 1:1. The electrospray ionization time-of-flight mass spectrum of the complex also provided clear evidence for the 2:1 complexation.     

Inversion of DNA helicity induced by zinc (II)-macrocyclic polyamine complexes

Abstract

Exposure of synthetic polynucleotide poly(dG-dC)·poly(dG-dC) to Zn^II cyclen, 2 (cyclen = 1,4,7,10-tetraazacyclododecane), produces a dramatic change in its circular dichroism (CD) spectrum in H₂O at pH 7.2, 24°C: the CD spectrum of the initial B form changes to that of the Z form (or a non-Z structure with a left-handed helix) at very low concentrations ([Zn^II]/[base pair] in molar basis ≤ 1). By contrast, Zn^II-[12]aneN₃, 1 ([12]aneN₃ = 1,5,9-triazacyclododecane), and Zn^II-cyclam, 3 (cyclam = 1,4,8,11-tetraazacyclo-tetradecane), do not significantly have such a topological affect on the polynucleotide even at much higher concentrations. An increase in Na⁺ ionic strength nullified the effect of 2 on the CD spectrum, indicating an outside interaction (electrostatic and/or hydrogen bonding) of the DNA model. This study illustrates the significance of the macrocyclic ligand structure around the Zn^II ion for specific interaction with DNA.