Investigation of the Structure and Dynamics of the Capsid–Spacer Peptide 1–Nucleocapsid Fragment of the HIV‐1 Gag Polyprotein by Solution NMR Spectroscopy

Structural studies of HIV‐1 Gag, the primary structural polyprotein involved in retroviral assembly, have been challenging, owing to its flexibility and conformational heterogeneity. Using residual dipolar couplings, we show that the four structural units of the capsid (CA)–spacer peptide 1 (SP1)–nucleocapsid (NC) fragment of HIV‐1 Gag (namely, the N‐ and C‐terminal domains of capsid, and the N‐ and C‐terminal Zn knuckles of nucleocapsid) have the same structures as their individually isolated counterparts, and tumble semi‐independently of one another in the absence of nucleic acids. Nucleic acids bind exclusively to the nucleocapsid domain and fix the orientation of the two Zn knuckles relative to one another so that the nucleocapsid domain/nucleic acid complex behaves as a single structural unit. The low ¹⁵N–{¹H} heteronuclear NOE values (≤0.4), the close to zero values for the residual dipolar couplings of the backbone amides, and minimal deviations from random‐coil chemical shifts for the C‐terminal tail of capsid and SP1, both in the absence and presence of nucleic acids, indicate that these regions are intrinsically disordered in the context of CA–SP1–NC.     

An Investigation of Poly(dimethylsiloxane) Chain Dynamics and Order in Its Inclusion Compound with γ‐Cyclodextrin by Fast‐MAS Solid‐State NMR Spectroscopy

The dynamics of poly(dimethylsiloxane) in its inclusion compound with γ‐cyclodextrin are elucidated using modern fast‐MAS solid‐state NMR techniques. Measurements of methyl ¹H–¹H and ¹H–¹³C dipolar coupling constants indicate that the polymer undergoes a uniform motion, rendering all methyl groups equivalent. The dynamics of the Si—C bond is characterized by either a dynamic order parameter of S = 0.72, or, assuming a stably rotating helical structure, an inclination angle of 73° relative to the rotation axis.     

Application of Weakly Oriented Non‐ionic Liquid Crystal Solvents to NMR Studies of Poly‐ethylene Oxide (PEO)

We report in this article the application of a series of weakly ordered liquid crystal solvents for liquid state nuclear magnetic resonance (NMR) spectroscopy. The solvents are a n‐alkyl‐poly(ethylene glycol)/n‐alkyl alcohol non‐ionic liquid crystal system, first proposed by Ruckert and Otting (J. Am. Chem. Soc. 2000 , 122, 7793). The merits of these solvents are further demonstrated by using them with a homogeneous polymer PEO which is one of the most studied polymer electrolyte materials, thus offering an answer to the question of whether the weak anisotropy introduced by liquid crystal solvents has any connection with the large‐scale (≥ one nanometer) heterogeneity (tertiary or higher orders of structure) of the system under study.     

13C NMR investigations of molecular order of rod-like,bent-core,and thiophene mesogens

In this review, methods to obtain the orientational order of topologically variant molecular mesogens using by one- and two-dimensional (2D) solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy are described. Besides ¹³C chemical shifts, the ¹³C─¹H dipolar couplings measured from 2D-separated local field (SLF) technique are used for computing the order parameters of a variety of mesogens. The investigated molecules are composed of a variable number of rings in the core, that is, core ranging from simply one ring to five rings. Among the mesogens investigated, a special focus has been placed on mesogens with thiophene rings, which are gaining popularity as liquid crystalline organic semiconductors. The replacement of a phenyl ring by thiophene in the core has a dramatic influence on molecular topology, as observed from the measured order parameters. The review highlights the advantages of the 2D SLF method for understanding the local dynamics and for mapping the topology of mesogens through the measured order parameters. SLF NMR studies of as many as 24 molecular mesogens that vary in terms of the molecular structure as well as topology are covered in the review. Order parameters of the rings have been estimated from the ¹³C─¹H dipolar couplings in the nematic, smectic A, smectic C, and tilted hexatic phases as well as in B₁ and B₂ mesophases of various mesogens. It is anticipated that, in the years to come, the 2D SLF method would provide advanced molecular information on structurally complex mesogens that are emerging in liquid crystal science through the incessant efforts of synthetic chemists. The mini review covers the orientational order of topologically variant molecular mesogens determined by 1D and 2D solid-state ¹³C NMR spectroscopy. Accordingly, rod-like, bent-core, and thiophene mesogens were subjected to 2D SLF measurements to get the order parameters from which the topology was established. The replacement of phenyl ring by thiophene and its influence on order parameters as well as on molecular topology is also discussed.     

Determination of Configuration and Conformation of a Reserpine Derivative with Seven Stereogenic Centers Using Molecular Dynamics with RDC-Derived Tensorial Constraints**

NMR-based determination of the configuration of complex molecules containing many stereocenters is often not possible using traditional NOE data and coupling patterns. Making use of residual dipolar couplings (RDCs), we were able to determine the relative configuration of a natural product containing seven stereocenters, including a chiral amine lacking direct RDC data. To identify the correct relative configuration out of 32 possible ones, experimental RDCs were used in three different approaches for data interpretation: by fitting experimental data based singular value decomposition (SVD) using a single alignment tensor and either (i) a single conformer or (ii) multiple conformers, or alternatively (iii) using molecular dynamics simulations with tensorial orientational constraints (MDOC). Even though in all three approaches one and the same configuration could be selected and clear discrimination between possible configurations was achieved, the experimental data was not fully satisfied by the methods based on single tensor approaches. While these two approaches are faster, only MDOC is able to fully reproduce experimental results, as the obtained conformational ensemble adequately covers the conformational space necessary to describe the molecule with inherent flexibility.     

Direct estimation of an element of order matrix from 1H NMR spectra of strongly dipolar coupled spins

NMR spectra of molecules oriented in thermotropic liquid crystalline media provide information on the molecular structure and order. The spins are generally strongly dipolar coupled and the spectral analyses require the tedious and time consuming numerical iterative calculations. The present study demonstrates the application of multiple quantum spin state selective detection of single quantum transitions for mimicking the homonuclear decoupling and the direct estimation of an element of ordering matrix. This information is utilized to estimate the nearly accurate starting dipolar couplings for iterative calculations. The studies on the spectra of strongly dipolar coupled five and six interacting spin systems are reported. Copyright © 2009 John Wiley & Sons, Ltd.     

Exploring the Conformational Space of Bridge‐Substituted Dithienylcyclopentenes

Stimuli responsive compounds and materials are of high interest in synthetic chemistry and materials science, with light being the most intriguing stimulus due to the possibility to remote control the physicochemical properties of a molecule or a material. There is a constant quest to design photoswitches with improved switching efficiency and especially diarylethene‐type switches promise photo cyclization quantum yields up to unity. However, only limited attention has been paid towards the influence of the solution conformation on the switching efficiency. Here, we describe a detailed NMR spectroscopic investigation on the conformational distribution of bridge‐substituted dithienylcyclopentenes in solution. We could discriminate between several photoactive and photoinactive as well as two diastereomorphous conformations and show that the trends observed in the switching efficiency match the conformer populations obtained from state of the art NMR parameters in solution.     

Isobutylene‐rich macromonomers: Dynamics and yields of peroxide‐initiated crosslinking

New isobutylene‐rich elastomers bearing multiple pendant styrenic, acrylic, maleimidic, vinylic, and allylic functional groups have been prepared and examined in the context of peroxide‐initiated crosslinking. Halide displacement from brominated poly(isobutylene‐co‐isoprene) (BIIR) by the requisite carboxylate nucleophiles in homogeneous toluene solutions provide the desired esters in quantitative yield without complications from dehydrohalogenation or premature crosslinking. Heating the resulting macromonomers with dicumyl peroxide to 160 °C under solvent‐free conditions gives thermoset derivatives, with reaction rates and yields depending markedly on functional group structure. In general, high cure extents can only be achieved using highly reactive pendant functional groups, owing to the competitive balance between crosslinking through C?C oligomerization, and degradation through β‐scission of backbone macroradical intermediates. Independent control of crosslinking rates and cure extents is gained through the use of nitroxyl radical traps bearing acrylate functionality. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 123–132     

Relative and Absolute Configuration of Vatiparol (1 mg): A Novel Anti‐inflammatory Polyphenol

Bioactive natural products offer multiple opportunities for the discovery of novel chemical entities with potential pharmaceutical, nutraceutical and agrochemical applications. Many new organic compounds with novel scaffolds are isolated in small quantities and established methods often fail to determine the structure and bioactivity of such novel natural products. To meet this challenge, we present here a new methodology combining RDC (residual dipolar coupling)‐based NMR spectroscopy in microtubes, with a motif‐inspired biological assessment strategy. Using only one milligram (ca. 1.5 μmol) of sample, the new protocol established the bioactivity as well as the relative and absolute configuration of vatiparol obtained from Vatica parvifolia. Vatiparol is unique in its unprecedented carbon skeleton and selective inhibitory effect on the expression of monocyte chemo‐attractant protein‐1 (MCP‐1, also known as CCL2). The plausible biosynthetic pathway of vatiparol is briefly discussed. The approach introduced here promises to be widely applicable to the determination of the structure and bioactivity of structurally unknown organic samples available in very limited amounts.     

Synthesis and characterization of novel PDMS nanocomposites using POSS derivatives as cross‐linking filler

We report the synthesis and characterization of novel elastomeric nanocomposites containing polyhedral oligomeric silsesquioxanes (POSS) as both the cross‐linker and filler within a polydimethylsiloxane (PDMS) polymer matrix. These polymer composites were prepared through the reaction of octasilane‐POSS (OS‐POSS) with vinyl‐terminated PDMS chains using hydrosilylation chemistry. In addition, larger super‐POSS cross‐linkers, consisting of two pendant hepta(isobutyl)POSS molecules attached to a central octasilane‐POSS core, were also used in the fabrication of the PDMS composites. The chemical incorporation of these POSS cross‐linkers into the PDMS network was verified by solid‐state ¹H magic angle spinning NMR. Based on dynamic mechanical analysis, the PDMS nanocomposites prepared with the octafunctional OS‐POSS cross‐linker exhibited enhanced mechanical properties relative to polymer systems prepared with the tetrafunctional TDSS cross‐linker at equivalent loading levels. The observed improvements in mechanical properties can be attributed to the increased dimensionality of the POSS cross‐linker. The PDMS elastomers synthesized from the larger super‐POSS molecule showed improved mechanical properties relative to both the TDSS and OS‐POSS composites due to the increased volume‐fraction of POSS filler in the polymer matrix. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2589–2596, 2009     

Conformational Analysis of the Anti‐obesity Drug Lorcaserin in Water: How To Take Advantage of Long‐Range Residual Dipolar Couplings

The conformational state of 8‐chloro‐1‐methyl‐2,3,4,5‐tetrahydro‐1H‐3‐benzazepine hydrochloride (lorcaserin) in water has been determined on the basis of one‐bond and long‐range C? H residual dipolar coupling (RDC) data along with DFT computations and ³J_HH coupling‐constant analysis. According to this analysis, lorcaserin exists as a conformational equilibrium of two crown‐chair forms, of which the preferred conformation has the methyl group in an equatorial orientation.     

Collection of NMR Scalar and Residual Dipolar Couplings Using a Single Experiment

A new DMSO‐compatible aligning gel based on cross‐linked poly(2‐hydroxylethyl methacrylate) (poly‐HEMA) has been developed. Due to a significant difference in bulk magnetic susceptibility between the DMSO inside and outside the gel, it is possible to simultaneously collect isotropic and anisotropic NMR data, such as residual dipolar couplings (RDC), in the same NMR tube. RDC‐assisted structural analysis of menthol and the alkaloid retrorsine is reported as proof of concept.     

Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings.

Despite the importance of molecular dynamics for biological activity, most approaches to protein structure determination, whether based on crystallographic or solution studies, propose three-dimensional atomic representations of a single configuration that take no account of conformational fluctuation. Non-averaged anisotropic NMR interactions, such as residual dipolar couplings, that become measurable under conditions of weak alignment, provide sensitive probes of both molecular structure and dynamics. Residual dipolar couplings are becoming increasingly powerful for the study of proteins in solution. In this minireview we present their use for the simultaneous determination of protein structure and dynamics.     

Current developments in homonuclear and heteronuclear J‐resolved NMR experiments

Two‐dimensional J‐resolved (Jres) NMR experiments offer a simple, user‐friendly spectral representation where the information of coupling constants and chemical shifts are separated into two orthogonal frequency axis. Since its initial proposal 40 years ago, Jres has been the focus of considerable interest both in improving the basic pulse sequence and in its successful application to a wide range of studies. Here, the latest developments in the design of novel Jres pulse schemes are reviewed, mainly focusing on obtaining pure absorption lineshapes, minimizing strong coupling artifacts, and also optimizing sensitivity and experimental measurements. A discussion of several Jres versions for the accurate measurement of a different number of homonuclear (J_HH) and heteronuclear (J_CH) coupling constants is presented, accompanied by some illustrative examples.