Solution NMR spectroscopy of supra-molecular systems, why bother? A methyl-TROSY view

With the development of appropriate labeling schemes and the associated experiments that exploit them it has become possible to record high quality solution NMR spectra of supra-molecular complexes with molecular masses extending to 1MDa. One such approach involves selective (13)CH(3) methyl labeling in highly deuterated proteins using experiments that make use of a methyl-TROSY effect that significantly improves both resolution and sensitivity in spectra. The utility of this methodology has been demonstrated on a growing number of interesting particles. It seems appropriate at this juncture, therefore, to 'step back' and evaluate the role that solution NMR spectroscopy can play in what has traditionally been the domain of X-ray crystallography and more recently cryo-electron microscopy. It is argued here that solution NMR can make a critical contribution to our understanding of how dynamics regulate function in these high molecular weight systems. Several examples from work in my laboratory on the proteasome are presented as an illustration.     

A review of: “Ordering in strongly fluctuating condensed matter systems”

Abstract

Ed. T. Riste. (Nato Advanced Study Institutes Series, Vol. 50). Plenum, Price: $55 (U.S.)     

Rotational band contour analysis in the à 1 A′-[Xtilde] 1 A′ electronic systems of substituted naphthalenes

The 0₀ ⁰ bands of the à ¹ A′-[Xtilde] ¹ A′ electronic systems of 2-fluoro, 2-hydroxy- and 2-aminonaphthalene have been identified and then rotationally analysed by the method of rotational band contour analysis. The effect of 2-substitution on the direction of the electronic transition moment vector in naphthalene is found to be drastic: the vector is oriented by about 70–80° (anti-clockwise in figure 1) by the substituent. However, the orientation is almost unaffected by the nature of the substituent.

The 0₀ ⁰ bands are all type A, B hybrids but predominantly type B. Significant differences in the 0₀ ⁰ band rotational contours in the three molecules are reflected in the different values of ΔA, ΔB and ΔC found from the contour analyses. An attempt to interpret the changes of rotational constants in terms of changes in geometry from the ground to the excited state suggest very strongly that the geometry change of the naphthalene rings in all the molecules is similar to that in naphthalene itself but that the carbon-substituent bonds contract in the excited state. The contraction increases from F to OH to NH₂ and is probably quantitatively similar to that suggested previously for the corresponding monosubstituted benzenes.     

Rotational band contour analysis in the Ã1A′-[Xtilde]1A′ electronic systems of substituted naphthalenes

The 0₀ ⁰ bands of the à ¹ A′-[Xtilde] ¹ A′ systems of 1-fluoro, 1-hydroxy and 1-aminonaphthalene have been investigated by rotational band contour analysis. The 0₀ ⁰ bands in 1-fluoro and 1-hydroxynaphthalene are 70 per cent type A and 30 per cent type B, and 75 per cent type A and 25 per cent type B hybrids respectively: the electronic transition moment vector has been rotated by about 15° towards the carbon atom C₃ by the F and OH substituents compared to naphthalene (in which, in the Ã-[Xtilde] system, it is along the long in-plane axis). In 1-aminonaphthalene it seems likely that the 0₀ ⁰ band is predominantly type A, but it could not be observed with sufficient intensity to be able to obtain the excited state rotational constants with any certainty.     

Stars of strange matter?

We investigate suggestions that quark matter with strangeness per baryon of order unity may be stable. We model this matter at nuclear matter densities as a gas of close packed Λ-particles. From the known mass of the Λ-particle we obtain an estimate of the energy and chemical potential of strange matter at nuclear densities. These are sufficiently high to preclude any phase transition from neutron matter to strange matter in the region near nucleon matter density. Including effects from gluon exchange phenomenologically, we investigate higher densities, consistently making approximations which underestimate the density of transition. In this way we find a transition density ρ_tr≳7ρ₀, where ρ₀ is nuclear matter density is not far from the maximum density in the center of the most massive neutron stars that can be constructed. Since we have underestimated ρ_tr and still find it to be ∼7ρ₀, we do not believe that the transition from neutron to quark matter is likely in neutron stars. Moreover, measured masses of observed neutron stars are ≅1.4 M_⊙, where M_⊙ is the solar mass. For such masses, the central (maximum) density is ρ_c<5ρ₀. Transition to quark matter is certainly excluded for these densities.     

Time dependence of hysteresis loop displacement in hard–soft magnetic systems

Time dependence of the hysteresis loop asymmetry observed in partially crystallized _{Co66Si16B12Fe4Mo2}${\mathrm{Co}}_{66}{\mathrm{Si}}_{16}{\mathrm{B}}_{12}{\mathrm{Fe}}_4{\mathrm{Mo}}_2$ is here analyzed at room temperature. The results are related to a magnetic aftereffect occurring in the hard crystallites embedded in the residual soft matrix. The coercive field is found to be constant with time, which is explained in terms of the dipolar interaction theory.     

Comparison of the calculated electronic structures of [111] and [001] GaAs/AℓxGa1-xAs semiconductor superlattices

A theoretical comparison of the electronic structures of long-period (about 300 Å) N_GaAs×N_AℓGaAs GaAs/Aℓ_0.3Ga_0.7As superlattices grown along the [111] direction and superlattices grown along the [001] direction is presented. Almost all qualitative features of the theoretical results are in good agreement with experiments by Hayakawa et al. The observed optical transition enhancement in the [111]-oriented quantum-well structures is caused by the topological difference in the superlattices, and is only partly due to the fact that the heavy holes in the [111] superlattices have larger transverse effective masses, and therefore have larger two-dimensional valence band densities of states.     

Remanence characteristic of nanostructure of hard/soft magnetic multilayered systems with random easy axis orientations

The macroscopic magnetic properties such as remanent magnetization of the ferromagnetic multilayer system with random easy axis orientations is investigated by using a effective micromagnet approach. The multilayer, which alternating soft/hard layers in which their easy axis orientations is random build a nanostructured multilayer, is considered to meet periodic boundary condition, the dependence of remanence on thickness has been analytical derived. Author find that the remancence clearly depends on the thickness of the soft magnetic layer nearly independence of thickness of hard magnetic layer. this analytical results are in excellent agreement with previous numerical results.     

Gold(I)-assisted catalysis – a comprehensive view on the [3,3]-sigmatropic rearrangement of allyl acetate

ABSTRACT

The unified reaction valley approach (URVA) combined with the local mode, ring puckering and electron density analysis is applied to elucidate the mechanistic differences of the non-catalysed and the Au[I]-N-heterocyclic carbene (NHC)-catalysed [3,3]-sigmatropic rearrangement of allyl acetate. Using a dual-level approach (DFT and DLPNO-CCSD(T)), the influence of solvation, counter-ions, bulky and electron withdrawing/donating substituents as well as the exchange of the Au[I]-NHC with a Au[I]-phosphine catalyst is investigated. The catalyst breaks up the rearrangement into two steps by switching between Au[I]–π and Au[I]–σ complexation, thus avoiding the energy-consuming CO cleavage in the first step. Based on local stretching force constants k^a(C=C), we derive for the first time a quantitative measure of the π-acidity of the Au[I] catalyst; in all catalysed reactions, the bond order n(C=C) drops from 2 to 1.65. The ring puckering analysis clarifies that all reactions start and end via a six-membered ring with a boat form. All Au[I]–σ-complex intermediates show a considerable admixture of the chair form. The non-catalysed [3,3]-sigmatropic rearrangement goes through a maximum of charge separation between the allyl and acetate units at the transition state, while all catalysed reactions proceed via a minimum of charge separation reached in the region of the Au[I]–σ-complex.     

Width of the ? meson in nuclear matter

The ratios of the cross sections for ?-meson production induced by 2.83-GeV protons on Cu, Ag, and Au nuclei to the respective cross section for C nuclei were measured at the ANKE-COSY facility in the momentum range of 0.6?C1.6 GeV/c and the angular range of 0°?C8°. The product ? mesons were identified by their decay ? ?? K ⁺ K ^?. The procedure used to separate kaon pairs was described in detail, and all sources of the background and their contribution to the resulting error in the values found for the above cross-section ratios were analyzed. The A dependence of the cross section for ?-meson production was shown to obey the A ^0.56±0.03 law. The total width of the ? meson at a normal nuclear density was extracted from a comparison of the measured cross-section ratios with the results of calculations based on two theoretical models. The resulting width value exceeds substantially both the vacuum width and the width expected in the absence of the nuclear-matter effect on the properties of the ? meson.     

A soft matter in construction – Statistical physics approach to formation and mechanics of C–S–H gels in cement

Calcium-silicate hydrate (C–S–H) is the main binding agent in cement and concrete. It forms at the beginning of cement hydration, it progressively densifies as cement hardens and is ultimately responsible of concrete performances. This hydration product is a cohesive nano-scale gel, whose structure and mechanics are still poorly understood, in spite of its practical importance. Here we review some of the open questions for this fascinating material and a statistical physics approach recently developed, which allows us to investigate the gel formation under the out-of-equilibrium conditions typical of cement hydration and the role of the nano-scale structure in C–S–H mechanics upon hardening. Our approach unveils how some distinctive features of the kinetics of cement hydration can be related to changes in the morphology of the gels and elucidates the role of nano-scale mechanical heterogeneities in the hardened C–S–H.     

Phonon dispersion relations and soft modes of 4? carbon nanotubes

The phonon dispersion relations of three kinds of 4~? carbon nanotubes are calculated by using the density functional perturbation theory. It is found that the frequencies of some phonon modes are very sensitive to the smearing width used in the calculations, and eventually become negative at low electronic temperature. Moreover, two kinds of soft modes are identified for the (5,0) tube which are quite different from those reported previously. Our results suggest that the (5,0) tube remains metallic at very low temperature, instead of the metallic-semiconducting transition claimed before.     

Are halos of collisionless cold dark matter collisionless?

We study whether gravitational scattering of halo dark matter particles by subhalos can connect two seemingly independent problems: the abundance of subhalos in dark matter halos and the cuspiness of the halos' inner density profiles. Our numerical experiments indicate that subhalos can cause the collisionless dark matter particles in the centers of main halos to diffuse. Combined with tidal mass loss of the subhalos, this process introduces significant scatter in the inner density profiles and offers an explanation for the range of profiles seen in both observations and cosmological simulations.     

A facile one-pot ultrasound assisted for an efficient synthesis of 1H-spiro[furo[3,4-b]pyridine-4,3′-indoline]-3-carbonitriles

A convenient one-pot protocol was developed for the synthesis of 1H-spiro[furo[3,4-b]pyridine-4,3′-indoline]-3-carbonitrile derivatives. This reaction was carried out through a three component condensation reaction of isatins, malononitrile, and anilinolactones in the presence of a catalytic amount of Et₃N as an inexpensive and available basic catalyst in THF under ultrasound irradiation. The products were obtained in high yields and short reaction times. The main advantage of this synthetic method is that the obtained products in ultrasonic irradiations are different from classical heating.