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.     

Simultaneous Arrangement of up to Three Different Molecules on the Pore Surface of a Metal–Macrocycle Framework: Cooperation and Competition

Porous crystals are excellent materials with potential spatial functions through molecular encapsulation within the pores. Co‐encapsulation of multiple different molecules further expands their usability and designability. Herein we report the simultaneous arrangement of up to three different guest molecules, TTF (tetrathiafulvalene), ferrocene, and fluorene, on the pore surfaces of a porous crystalline metal–macrocycle framework (MMF). The position and orientation of adsorbed molecules arranged in the pore were determined by single‐crystal X‐ray diffraction analysis. The anchoring effect of hydrogen bonds between the hydroxy groups of the guest molecules and inter‐guest cooperation and competition are significant factors in the adsorption behaviors of the guest molecules. This finding would serve as a design basis of multicomponent functionalized nanospaces for elaborate reactions that are realized in enzymes.     

Ti(IV)-centered dynamic interconversion between Pd(II), Ti(IV)-containing ring and cage molecules

Heteronuclear, supramolecular ring and cage complexes have been constructed from a pyridyl catechol ligand, TiO(acac)2, and PdCl2(CH3CN)2. These two complexes are quantitatively interconvertible, in which Ti4+-centered coordination changes take place between a well-known Ti(catecholato)3 and a newly established TiH(catecholato)2(acetylacetonato) structures. The Ti4+-centered structural changes arise from the changes in the component fraction and basicity condition.     

Ion core structure in (C(2)n+ and (CS2)n- (n=3-10) studied by infrared photodissociation spectroscopy

Infrared photodissociation spectra of (CS(2))(n) (+) and (CS(2))(n) (-) with n=3-10 are measured in the 1100-2000 cm(-1) region. All the (CS(2))(n) (+) clusters exhibit three bands at approximately 1410, approximately 1490, and approximately 1540 cm(-1). The intensity of the 1540 cm(-1) band relative to those of the other bands increases with increasing the cluster size, indicating that the band at 1540 cm(-1) is assignable to the antisymmetric CS stretching vibration of solvent CS(2) molecules in the clusters. On the basis of density functional theory calculations, the 1410 and 1490 cm(-1) bands of (CS(2))(n) (+) are assigned to CS stretching vibrations of the C(2)S(4) (+) cation core with a C(2) form. The (CS(2))(n) (-) clusters show two bands at around 1215 and 1530 cm(-1). Similar to the case of cation clusters, the latter band is ascribed to the antisymmetric CS stretching vibration of solvent CS(2) molecules. Vibrational frequency analysis of CS(2) (-) and C(2)S(4) (-) suggests that the 1215 cm(-1) band is attributed to the antisymmetric CS stretching vibration of the CS(2) (-) anion core with a C(2v) structure.     

Conformation of L-tyrosine studied by fluorescence-detected UV-UV and IR-UV double-resonance spectroscopy

The laser-induced fluorescence spectrum of jet-cooled L-tyrosine exhibits more than 20 vibronic bands in the 35450-35750 cm(-1) region. We attribute these bands to eight conformers by using results of UV-UV hole-burning spectroscopy. These isomers are classified into four groups; each group consists of two rotational isomers that have a similar side-chain conformation but different orientations of the phenolic OH. The splitting of band origins of rotational isomers is 31, 21, 5, and 0 cm(-1) for these groups. IR-UV spectra suggest that conformers belonging to two of the four groups have an intramolecular OH...N hydrogen bond between the COOH and NH2 groups. By comparing experimental and theoretical results of L-tyrosine with those of L-phenylalanine, we propose probable conformers of L-tyrosine.     

A template-directed synthetic approach to halogen-bridged mixed-valence platinum complexes on artificial peptides in solution

A template-directed synthetic approach to halogen-bridged mixed-valence platinum complexes has been performed in organic media using, for instance, a synthetic peptide bearing two bis(ethylenediamine)-based Pt(IV) complexes with two axial bromide anionic ligands, [(Pt(IV)Br2(en))2](RSO3)4, and a [Pt(II)(en)2](RSO3)2 complex (R = (C12H25OCH2)2CHO(CH2)3-).     

Picosecond IR-UV pump-probe spectroscopic study on the vibrational energy flow in isolated molecules and clusters

Intramolecular vibrational energy redistribution (IVR) and vibrational predissociation (VP) from the XH stretching vibrations, where X refers to O or C atom, of aromatic molecules and their hydrogen(H)-bonded clusters are investigated by picosecond time-resolved IR-UV pump probe spectroscopy in a supersonic beam. For bare molecules, we mainly focus on IVR of the OH stretch of phenol. We describe the IVR of the OH stretch by a two-step tier model and examine the effect of the anharmonic coupling strength and the density of states on IVR rate and mechanism by using isotope substitution. In the H-bonded clusters of phenol, we show that the relaxation of the OH stretching vibration can be described by a stepwise process and then discuss which process is sensitive to the H-bonding strength. We discuss the difference/similarity of IVR/VP between the "donor" and the "acceptor" sites in phenol-ethylene cluster by exciting the CH stretch vibrations. Finally, we study the vibrational energy transfer in the isolated molecules having the alkyl chain, namely phenylalcanol (PA). In this system, we measure the rate constant of the vibrational energy transfer between the OH stretch and the vibrations of benzene ring which are connected at the both ends of the alkyl chain. This energy transfer can be called "through-bond IVR". We investigate the three factors which are thought to control the energy transfer rate; (1) "OH <--> next CH(2)" coupling, (2) chain length and (3) conformation. We discuss the energy transfer mechanism in PAs by examining these factors.     

Iridium‐Catalyzed Reductive Carbon–Carbon Bond Cleavage Reaction on a Curved Pyridylcorannulene Skeleton

The cleavage of C? C bonds in π‐conjugated systems is an important method for controlling their shape and coplanarity. An efficient way for the cleavage of an aromatic C? C bond in a typical buckybowl corannulene skeleton is reported. The reaction of 2‐pyridylcorannulene with a catalytic amount of IrCl₃?n H₂O in ethylene glycol at 250 °C resulted in a structural transformation from the curved corannulene skeleton to a strain‐free flat benzo[ghi]fluoranthene skeleton through a site‐selective C? C cleavage reaction. This cleavage reaction was found to be driven by both the coordination of the 2‐pyridyl substituent to iridium and the relief of strain in the curved corannulene skeleton. This finding should facilitate the design of carbon nanomaterials based on C? C bond cleavage reactions.     

Isomer selective IR-UV depletion spectroscopy of 4-fluorotoluene-NH3: evidence for π-proton-acceptor and linear hydrogen-bonded complexes

The 4-fluorotoluene-ammonia van der Waals complex has been studied using IR-UV depletion and hole-burning spectroscopies with assignments supported by ab initio and DFT calculations of ground state binding energies and intramolecular vibrational frequencies. The experimental IR-UV depletion and hole-burning spectra presented here provide unequivocal empirical evidence that the 4FT-NH(3) complex exists in two almost equally stable conformational forms. Both isomers contribute intensity to the experimental R2PI spectrum with one responsible for bands appearing to the red of the 4FT band origin position, and the other for those appearing immediately to the blue. On the basis of comparison of computed NH stretching frequencies with those obtained from the IR-UV spectra, the red-shifted bands are assigned to a π-proton-acceptor complex featuring an NH···π-hydrogen bond, and the blue-shifted bands are assigned to an in-plane σ-complex in which the ammonia binds in the plane of the ring forming a double-hydrogen-bonded six-membered ring with the fluorine atom. Ground state interaction energies computed at the M06-2X/cc-pVTZ level were found to compare favourably with those obtained at the CCSD(T) CBS level, although the former resulted in overbinding of the π-complex compared with the in-plane conformer, a characteristic shared with MP2 level calculations. The observation of a π-complex in addition to a σ-complex is consistent with the conclusion that the electron-donating power of the methyl group is sufficiently large to counter-balance the electron-withdrawing power of the fluorine atom.