Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.     

Crystallographic and Dynamic Aspects of Solid‐State NMR Calibration Compounds: Towards ab Initio NMR Crystallography

The excellent results of dispersion‐corrected density functional theory (DFT‐D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT‐D calculations is a target, especially for the field of molecular NMR crystallography. Four ¹³C ss‐NMR calibration compounds are investigated by single‐crystal X‐ray diffraction, molecular dynamics and DFT‐D calculations. The crystal structure of 3‐methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated ¹³C chemical shifts of these compounds are in excellent agreement with experiment, with a root‐mean‐square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT‐D chemical shift calculation improves the accuracy of calculated chemical shifts.     

Geometry dependence of spin-spin couplings in cyanamide by DFT analysis.

There have been numerous theoretical and experimental investigations examining NMR parameters related to non-amino N-H...N H-bonded moieties in both biological and chemical contexts. In contrast, little information on the geometry dependence of NMR parameters related to the biologically important H-bond donor amino group is available. Herein, the geometric dependencies of the one-bond amino N-H spin-spin coupling constants [(1)J(NH)] in the cyanamide monomer and dimer have been computed with B3LYP and the aug-cc-pVTZ-su0 basis set. In an isolated planar cyanamide molecule, the |(1)J(NH)| couplings were found to increase as the N-H bond lengthened. In contrast, in the planar cyanamide dimer the size of the H-bonded amino N-H coupling (|(1)J(N(d)H(d))|) decreased with increasing N(d)H(d) bond length. The |(1)J(N(d)H(d))| coupling was larger than the |(1)J(N(d)H(free))| coupling for N(d)H(d) distances up to 1.18 A (for a fixed N(d)H(free) distance of 1.006 A). Hence, the decrease of |(1)J(NH)| with increasing N-H distance, as well as the larger value of |(1)J(N(d)H(d))| compared to |(1)J(N(d)H(free))|, were only observed for situations where the amino group is involved in an H-bonding interaction. This is attributed to electron redistribution induced by the presence of the second cyanamide molecule. Similar electron-redistribution effects are thought to be responsible for the observed distance dependence of computed (1)J(NH) couplings of H-bonded amino groups in near-planar G-quartet structures. Here, the |(1)J(NH)| couplings of the amino N-H bonds decreased with increasing N-H bond length whereas the |(1)J(N(d)H(d))| couplings are approximately 7 Hz larger than the |(1)J(N(d)H(free))| couplings, despite the longer N(d)-H(d) bond length.     

A Photosensitive Liquid Crystal Studied by 14N NMR, 2H NMR,and DFT Calculations

An azobenzene derivative, namely diheptylazobenzene, showing the nematic and smectic A liquid crystalline phases, was investigated by means of a combined approach based on NMR and DFT calculations. ¹⁴N NMR quadrupole‐ and chemical‐shift‐perturbed spectra were acquired in the whole mesophasic range, providing both experimental quadrupolar splittings and chemical shift anisotropy values. On the same mesogen, deuterium labelled at the α‐position of the hydrocarbon chain, ²H NMR quadrupole‐perturbed spectra were recorded. The analysis of these NMR data was performed with the help of ab initio calculations, in vacuo and by taking into account the effect of the anisotropic environment typical of liquid crystals, by using the IEF‐PCM model. The geometry optimizations of the azomesogen in the trans and cis configurations were performed by DFT calculations employing the combination of B3LYP functional with the 6‐311G(d) basis set. The analysis of experimental NMR data was performed by considering the trans configuration as the most populated one and the corresponding quadrupolar tensors and chemical shielding tensors were determined at the DFT level of theory. The main result of this work is the determination of a relatively high and temperature‐dependent molecular biaxiality of the trans state of this azomesogen.     

NMR Crystallography of an Oxovanadium(V) Complex by an Approach Combining Multinuclear Magic Angle Spinning NMR,DFT, and Spin Dynamics Simulations

Bioinorganic vanadium(V) solids are often challenging for structural analysis. Here, we explore an NMR crystallography approach involving multinuclear ¹³C/⁵¹V solid‐state NMR spectroscopy, density functional theory (DFT), and spin dynamics numerical simulations, for the spectral assignment and the 3D structural analysis of an isotopically unmodified oxovanadium(V) complex, containing 17 crystallographically inequivalent ¹³C sites. In particular, we report the first NMR determination of C–V distances. So far, the NMR observation of ¹³C–⁵¹V proximities has been precluded by the specification of commercial NMR probes, which cannot be tuned simultaneously to the close Larmor frequencies of these isotopes (100.6 and 105.2 MHz for ¹³C and ⁵¹V, respectively, at 9.4 T). By combining DFT calculations and ¹³C–⁵¹V NMR experiments, we propose a complete assignment of the ¹³C spectrum of this oxovanadium(V) complex. Furthermore, we show how ¹³C–⁵¹V distances can be quantitatively estimated.     

Effects of Quantum Nuclear Delocalisation on NMR Parameters from Path Integral Molecular Dynamics

The influence of nuclear delocalisation on NMR chemical shifts in molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory calculations of shielding tensors. Nuclear quantum effects are shown to explain previously observed systematic deviations in correlations between calculated and experimental chemical shifts, with particularly large PIMD‐induced changes (up to 23 ppm) observed for carbon atoms in methyl groups. The PIMD approach also enables isotope substitution effects on chemical shifts and J couplings to be predicted in excellent agreement with experiment for both isolated molecules and molecular crystals. An approach based on convoluting calculated shielding or coupling surfaces with probability distributions of selected bond distances and valence angles obtained from PIMD simulations is used to calculate isotope effects.     

Spontaneous Double Hydrometallation Induced by N→M Coordination in Organometallic Hydrides of Group 14 Elements

Our attempts to synthesise N→M intramolecularly coordinated diorganometallic hydrides L₂MH₂ [M=Si ( 4 ), Ge ( 5 ), Sn ( 6 )] containing the CH=N imine group (in which L is C,N‐chelating ligand {2‐[(2,6‐iPr₂C₆H₃)N=CH]C₆H₄}^?) yielded 1,1′‐bis(2,6‐diisopropylphenyl)‐2,2′‐spriobi[benzo[c][1,2]azasilole] ( 7 ), 1,1′‐bis(2,6‐diisopropylphenyl)‐2,2′‐spriobi[benzo[c][1,2]azagermole] ( 8 ) and C,N‐chelated homoleptic stannylene L₂Sn ( 10 ), respectively. Compounds 7 and 8 are an outcome of a spontaneous double hydrometallation of the two CH=N imine moieties induced by N→M intramolecular coordination (M=Si, Ge) in the absence of any catalyst. In contrast, the diorganotin hydride L₂SnH₂ ( 6 ) is redox‐unstable and the reduction of the tin centre with the elimination of H₂ provided the C,N‐chelated homoleptic stannylene L₂Sn ( 10 ). Compounds 7 and 8 were characterised by NMR spectroscopy and X‐ray diffraction analysis. Because the proposed N→M intramolecularly coordinated diorganometallic hydrides L₂MH₂ [M=Si ( 4 ), Ge ( 5 ), Sn ( 6 )] revealed two different types of reduction reactions, DFT calculations were performed to gain an insight into the structures and bonding of the non‐isolable diorganometallic hydrides as well as the products of their subsequent reactions. Furthermore, the thermodynamic profiles of the different reaction pathways with respect to the central metal atom were also investigated.     

Berry pseudorotation mechanism for the interpretation of the 19F NMR spectrum in PF5 by ab initio molecular dynamics simulations.

For the first time, theoretical evidence that confirms the importance of the Berry pseudorotation process in the interpretation of the 19F NMR spectrum of phosphorus pentafluoride (PF5) is presented. Ab initio molecular dynamics simulations have been performed to generate a large number of configurations used for NMR parameter computations at the density functional theory level. Two different temperatures were set to highlight the effect of pseudorotation process on the NMR spectrum. Average 19F chemical shifts and spin-spin coupling constants calculated for the five fluorine atoms converge towards the NMR equivalence of the five atoms when the Berry pseudorotation mechanism is accounted for.     

Modeling of heavy-atom-ligand NMR spin-spin coupling in solution: molecular dynamics study and natural bond orbital analysis of Hg-C coupling constants

Ab initio molecular dynamics (MD) and relativistic density functional NMR methods were applied to calculate the one‐bond Hg? C NMR indirect nuclear spin–spin coupling constants (J) of [Hg(CN)₂] and [CH₃HgCl] in solution. The MD averages were obtained as J(¹⁹⁹Hg? ¹³C)=3200 and 1575 Hz, respectively. The experimental Hg? C spin–spin coupling constants of [Hg(CN)₂] in methanol and [CH₃HgCl] in DMSO are 3143 and 1674 Hz, respectively. To deal with solvent effects in the calculations, finite “droplet” models of the two systems were set up. Solvent effects in both systems lead to a strong increase of the Hg? C coupling constant. From a relativistic natural localized molecular orbital (NLMO) analysis, it was found that the degree of delocalization of the Hg 5d_σ nonbonding orbital and of the Hg? C bonding orbital between the two coupled atoms, the nature of the trans Hg? C/Cl bonding orbital, and the s character of these orbitals, exhibit trends upon solvation of the complexes that, when combined, lead to the strong increase of J(Hg? C).     

Towards the Accurate Calculation of 183W NMR Chemical Shifts in Polyoxometalates: The Relevance of the Structure

DFT calculations were carried out to study ¹⁸³W NMR chemical shifts in the family of the Keggin anions with formula α‐[XW₁₂O₄₀]^q? (X=B, Al, Si, P, Ga, Ge, As, Zn), in the β‐ and γ‐[SiW₁₂O₄₀]^4? geometric isomers, in the derivative Dawson anion [P₂W₁₈O₆₂]^6?, and in the most symmetrical Lindqvist [W₆O₁₉]^2? anion and its derivative [W₁₀O₃₂]^4?. In this article, we show that the geometry employed in the calculation of NMR chemical shifts in polyoxotungstates is extremely important if we want to be quantitative. Using very large basis sets of QZ4P quality and taking into account the conductor‐like screening model (COSMO) to account for solvent effects (aqueous and organic solutions), good geometries were found for the polyoxoanions. From these optimal geometries the ¹⁸³W NMR chemical shifts were computed with the more standard basis sets of TZP quality and including spin–orbit corrections inside the zero‐order regular approximation (ZORA) to describe the relativistic effects of the internal electrons. With this strategy the mean absolute error between experimental and theoretical values was found to be less than 10 ppm, which is similar to the experimental error. We also discuss how the geometry of the polyoxoanion influences on the shielding.     

Connecting Discrete Stereoclusters by Using DFT and NMR Spectroscopy: The Case of Nivariol

The structural determination of small organic molecules is mainly undertaken by using NMR techniques, although it is increasingly supplemented by using computational methods. NMR parameters, such as chemical shifts and coupling constants, are extremely sensitive indicators of local molecular conformation and are a source of structural evidence. However, their interpretation is fairly challenging in many circumstances, such as the case of the new polyether squalene derivative nivariol, the structure of which was elucidated by means of NMR spectroscopy and DFT calculations. The potential flexibility of this molecule and the high number of quaternary carbon atoms that it contains make its configurational assignment very difficult. Moreover, the relative configuration of four separated stereoclusters was established and subsequently connected by using NOE and J‐based analysis, as well as by a comparison of its experimental ¹³C NMR chemical shifts with the corresponding population‐weighted values, as calculated by using DFT methods. Limitations of these used approaches became apparent but were overcome by combining the two methods.     

First detection of a selenenyl fluoride ArSe-F by NMR spectroscopy: the nature of Ar2Se2/XeF2 and ArSe-SiMe3/XeF2 reagents

Arylselenenyl fluorides ArSeF are obtained from diselenides Ar2Se2 or arylselenotrimethylsilanes ArSe-SiMe3, and XeF2. They are detected by low-temperature 19F and 77Se NMR spectroscopy. Substitution in the ortho position of the aromatic ring to provide electronic or steric protection is a requirement for their formation. ArSe--F compounds decompose according to 3 ArSe-F-->[ArSe-SeF2Ar]+ArSe-F-->ArSeF3+Ar2Se2. Reaction energies for this disproportionation as well as that of the sulfur and tellurium homologues have been calculated with MP2, CCSD(T,) and B3 LYP methods. They were found to be increasingly exothermic in the sequence S相似文献   

Exploring the Molecular Structure of Imidazolium–Silica‐Based Nanoparticle Networks by Combining Solid‐State NMR Spectroscopy and First‐Principles Calculations

A DFT‐based molecular model for imidazolium–silica‐based nanoparticle networks (INNs) is presented. The INNs were synthesized and characterized by using small‐angle X‐ray scattering (SAXS), NMR spectroscopy, and theoretical ab initio calculations. ¹¹B and ³¹P HETCOR CP MAS experiments were recorded. Calculated ¹⁹F NMR spectroscopy results, combined with the calculated anion–imidazolium (IM) distances, predicted the IM chain density in the INN, which was also confirmed from thermogravimetric analysis/mass spectrometry results. The presence of water molecules trapped between the nanoparticles is also suggested. First considerations on possible π–π stacking between the IM rings are presented. The predicted electronic properties confirm the photoluminescence emissions in the correct spectral domain.     

Toward the complete prediction of the 1H and 13C NMR spectra of complex organic molecules by DFT methods: application to natural substances

The NMR parameters (1H and 13C chemical shifts and coupling constants) for a series of naturally occurring molecules have been calculated mostly with DFT methods, and their spectra compared with available experimental ones. The comparison includes strychnine as a test case, as well as some examples of recently isolated natural products (corianlactone, daphnipaxinin, boletunone B) featuring unusual and/or crowded structures and, in the case of boletunone B, being the subject of a recent revision. Whenever experimental spectra were obtained in polar solvents, the calculation of NMR parameters was also carried out with the Integral Equation-Formalism Polarizable Continuum Model (IEF-PCM) continuum method. The computed results generally show a good agreement with experiment, as judged not only by statistical parameters but also by visual comparison of line spectra. The origin of the remaining discrepancies is attributed to the incomplete modeling of conformational and specific solvent effects.     

Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis₂ complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis₂ is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems.     

Alkaline earth chloride hydrates: chlorine quadrupolar and chemical shift tensors by solid-state NMR spectroscopy and plane wave pseudopotential calculations

A series of alkaline earth chloride hydrates has been studied by solid-state (35/37)Cl NMR spectroscopy in order to characterize the chlorine electric field gradient (EFG) and chemical shift (CS) tensors and to relate these observables to the structure around the chloride ions. Chlorine-35/37 NMR spectra of solid powdered samples of pseudopolymorphs (hydrates) of magnesium chloride (MgCl(2).6H(2)O), calcium chloride (CaCl(2).2H(2)O), strontium chloride (SrCl(2), SrCl(2).2H(2)O, and SrCl(2).6H(2)O), and barium chloride (BaCl(2).2H(2)O) have been acquired under stationary and magic-angle spinning conditions in magnetic fields of 11.75 and 21.1 T. Powder X-ray diffraction was used as an additional tool to confirm the purity and identity of the samples. Chlorine-35 quadrupolar coupling constants (C(Q)) range from essentially zero in cubic anhydrous SrCl(2) to 4.26+/-0.03 MHz in calcium chloride dihydrate. CS tensor spans, Omega, are between 40 and 72 ppm, for example, Omega= 45+/-20 ppm for SrCl(2).6H(2)O. Plane wave-pseudopotential density functional theory, as implemented in the CASTEP program, was employed to model the extended solid lattices of these materials for the calculation of their chlorine EFG and nuclear magnetic shielding tensors, and allowed for the assignment of the two-site chlorine NMR spectra of barium chloride dihydrate. This work builds upon our current understanding of the relationship between chlorine NMR interaction tensors and the local molecular and electronic structure, and highlights the particular sensitivity of quadrupolar nucleus solid-state NMR spectroscopy to the differences between various pseudopolymorphic structures in the case of strontium chloride.