Ab Initio Study of Fine and Hyperfine Interactions in Triplet POH

Phosphorous-containing molecules have a great relevance in prebiotic chemistry in view of the fact that phosphorous is a fundamental constituent of biomolecules, such as RNA, DNA, and ATP. Its biogenic importance has led astrochemists to investigate the possibility that P-bearing species could have formed in the interstellar medium (ISM) and subsequently been delivered to early Earth by rocky bodies. However, only two P-bearing molecules have been detected so far in the ISM, with the chemistry of interstellar phosphorous remaining poorly understood. Here, in order to shed further light on P-carriers in space, we report a theoretical spectroscopic characterisation of the rotational spectrum of POH in its 3A″ ground electronic state. State-of-the-art coupled-cluster schemes have been employed to derive rotational constants, centrifugal distortion terms, and most of the fine and hyperfine interaction parameters, while the electron spin–spin dipolar coupling has been investigated using the multi-configuration self-consistent-field method. The computed spectroscopic parameters have been used to simulate the appearance of triplet POH rotational and ro-vibrational spectra in different conditions, from cold to warm environments, either in gas-phase experiments or in molecular clouds. Finally, we point out that the predicted hyperfine structures represent a key pattern for the recognition of POH in laboratory and interstellar spectra.

The Flexibility of Oligosaccharides Unveiled Through Residual Dipolar Coupling Analysis

The intrinsic flexibility of glycans complicates the study of their structures and dynamics, which are often important for their biological function. NMR has provided insights into the conformational, dynamic and recognition features of glycans, but suffers from severe chemical shift degeneracy. We employed labelled glycans to explore the conformational behaviour of a β(1-6)-Glc hexasaccharide model through residual dipolar couplings (RDCs). RDC delivered information on the relative orientation of specific residues along the glycan chain and provided experimental clues for the existence of certain geometries. The use of two different aligning media demonstrated the adaptability of flexible oligosaccharide structures to different environments.

Bimodal 1H Double Quantum Build-Up Curves by Fourier and Laplace-like Transforms on Aged Cross-Linked Natural Rubber

The 1H DQ Fourier and Laplace-like spectra for a series of cross-linked natural rubber (NR) samples naturally aged during six years are presented and characterized. The DQ build-up curves of these samples present two peaks which cannot be described by classical functions. The DQ Fourier spectra can be obtained after a numeric procedure which introduces a correction time which depends less on the chosen approximation, spin-½ and isolated CH2 and CH3 functional groups. The DQ Fourier spectra are well described by the distributions of the residual dipolar coupling correlated with the distribution of the end-to-end vector of the polymer network, and with the second and fourth van Vleck moments. The deconvolution of DQ Fourier spectra with a sum of four Gaussian variates show that the center and the width of Gaussian functions increase linearly with the increase in the cross-link density. The Laplace-like spectra for the natural aged NR DQ build-up curves are presented. The centers of four Gaussian distributions obtained via both methods are consistent. The differences between the Fourier and Laplace-like spectra consist mainly of the spectral resolution in the favor of Laplace-like spectra. The last one was used to discuss the effect of natural aging for cross-linked NR.

Protein functional dynamics from the rigorous global analysis of DEER data: Conditions, components, and conformations

The potential of spin labeling to reveal the dynamic dimension of macromolecules has been recognized since the dawn of the methodology in the 1960s. However, it was the development of pulsed electron paramagnetic resonance spectroscopy to detect dipolar coupling between spin labels and the availability of turnkey instrumentation in the 21st century that realized the full promise of spin labeling. Double electron-electron resonance (DEER) spectroscopy has seen widespread applications to channels, transporters, and receptors. In these studies, distance distributions between pairs of spin labels obtained under different biochemical conditions report the conformational states of macromolecules, illuminating the key movements underlying biological function. These experimental studies have spurred the development of methods for the rigorous analysis of DEER spectroscopic data along with methods for integrating these distributions into structural models. In this tutorial, we describe a model-based approach to obtaining a minimum set of components of the distance distribution that correspond to functionally relevant protein conformations with a set of fractional amplitudes that define the equilibrium between these conformations. Importantly, we review and elaborate on the error analysis reflecting the uncertainty in the various parameters, a critical step in rigorous structural interpretation of the spectroscopic data.

Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR

Labeling of biomolecules with a paramagnetic probe for nuclear magnetic resonance (NMR) spectroscopy enables determining long-range distance restraints, which are otherwise not accessible by classically used dipolar coupling-based NMR approaches. Distance restraints derived from paramagnetic relaxation enhancements (PREs) can facilitate the structure determination of large proteins and protein complexes. We herein present the site-directed labeling of the large oligomeric bacterial DnaB helicase from Helicobacter pylori with cysteine-reactive maleimide tags carrying either a nitroxide radical or a lanthanide ion. The success of the labeling reaction was followed by quantitative continuous-wave electron paramagnetic resonance (EPR) experiments performed on the nitroxide-labeled protein. PREs were extracted site-specifically from 2D and 3D solid-state NMR spectra. A good agreement with predicted PRE values, derived by computational modeling of nitroxide and Gd3+ tags in the low-resolution DnaB crystal structure, was found. Comparison of experimental PREs and model-predicted spin label-nucleus distances indicated that the size of the "blind sphere" around the paramagnetic center, in which NMR resonances are not detected, is slightly larger for Gd3+ (~14 Å) than for nitroxide (~11 Å) in 13C-detected 2D spectra of DnaB. We also present Gd3+-Gd3+ dipolar electron-electron resonance EPR experiments on DnaB supporting the conclusion that DnaB was present as a hexameric assembly.

Linear optical properties of a linear chain of interacting gold nanoparticles

In a Drude-like model for the conduction electrons of Metal Nanoparticles (MNPs) in a periodic linear chain, considering dipole-dipole interactions of adjacent particles, an analytical expression is derived for each particle permittivity for two different polarizations of incident light: parallel with and perpendicular to the chain line. A numerical analysis is carried out for a chain including 10 identical gold Nanoparticles (NPs) for two different sizes of NPs and two different host media of air and glass. It is shown that in the parallel case of polarization, interaction of NPs leads to a substantial increase in the extinction cross section and the red-shift of the Surface Plasmon Resonance (SPR) wavelength. In comparison with the linear properties of a single NP, the second and penultimate particles have the most increase in the extinction cross section and SPR wavelength displacement while the first and last particles experience the least variations due to the mutual interactions. For the perpendicular polarization, inversely, the dipolar coupling causes the decrease in extinction cross section of all particles and the blue-shift of SPR wavelength. For the parallel polarization, the absolute values of the real and imaginary parts of complex permittivity of each MNP decrease in comparison with the single particle case while they increase for the perpendicular state of polarization.

Excitation of Ultrashort Spin Waves via Spin-Cherenkov Effect in Magnetic Waveguides

The excitation of ultrashort wavelength spin waves via the spin-Cherenkov effect in magnetic waveguides is investigated via a micromagnetic modeling. The proposed excitation method is relatively simple and easily tunable. The excitation efficiency of the proposed scheme is obtained for different excitation pulse velocities and widths. A coupled waveguide system is also considered. In this case, the spin waves are excited in the first waveguide and then are transferred to the second one due to the dipolar coupling between waveguides. It is also shown that the excitation and transfer of excited spin waves have some limitations related to the dipolar coupling mechanism between the waveguides.

Quantifying the effects of long-range 13C-13C dipolar coupling on measured relaxation rates in RNA

Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove 13C-13C dipolar couplings that complicate 13C relaxation analyses. While these phenomena are well documented for sites with adjacent 13C nuclei (e.g. ribose C1′), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) 13C-13C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-13C/15N]-ATP or selectively [2-13C]-ATP labeled RNAs. Our simulations predict non-negligible 13C-13C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R1) relaxation rates in [U-13C/15N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R1 measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-13C/15N]-ATP or [2-13C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range 13C-13C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R1 rates in terms of motional models for large RNAs.