NMR Coupling Research Articles

Conformational analysis of (-)-pironetin and its docking, molecular dynamics, and covalent interaction with α-tubulin

Theoretical conformational analysis of (-)-pironetin, a potent inhibitor of tubulin assembly, was based on DFT NMR coupling constants, showing two solvent-dependent conformational families. Docking studies of the pironetin-tubulin complex revealed hydrogen bond interactions with αAsn249, αAsn258 and αLys352 and supported formation of a covalent adduct between the αLys352 and the β carbon atom of pironetin lactone ring. Saturation transfer difference NMR spectroscopy confirmed that pironetin binds to tubulin, while molecular dynamics exposed a distortion of the M-loop between the αIle274 and αLeu285, an essential region for molecular recognition between α-α and β-β units of protofilaments.

Search for a Strong, Virtually “No‐Shift” Hydrogen Bond: A Cage Molecule with an Exceptional OH⋅⋅⋅F Interaction

AbstractReported herein is the synthesis of a molecule containing an unusually strong hydrogen bond between an OH donor and a covalent F acceptor, a heretofore somewhat ill‐defined if not controversial interaction. This unique hydrogen bond is to a large extent a product of the tight framework of the rigid caged system. Remarkably, the interaction shows little to no perceptible shift in the OH stretch of the IR spectrum relative to appropriate nonhydrogen‐bound standards in fairly non‐interactive solvents. This fascinating example of what has been termed a virtual “no‐shift” hydrogen bond is investigated through NMR (coupling constants, isotopic chemical shift perturbations, proton exchange rates) and IR studies which all tell a consistent story.

Search for a strong, virtually "no-shift" hydrogen bond: a cage molecule with an exceptional OH⋅⋅⋅F interaction.

Reported herein is the synthesis of a molecule containing an unusually strong hydrogen bond between an OH donor and a covalent F acceptor, a heretofore somewhat ill-defined if not controversial interaction. This unique hydrogen bond is to a large extent a product of the tight framework of the rigid caged system. Remarkably, the interaction shows little to no perceptible shift in the OH stretch of the IR spectrum relative to appropriate nonhydrogen-bound standards in fairly non-interactive solvents. This fascinating example of what has been termed a virtual "no-shift" hydrogen bond is investigated through NMR (coupling constants, isotopic chemical shift perturbations, proton exchange rates) and IR studies which all tell a consistent story.

Aromatic versus heteroradialene character in extended thiophloroglucinol ligands and their trinuclear nickel(II) complexes.

Extended phloroglucinol ligands and complexes are best described as nonaromatic heteroradialenes. Herein, the electronic structures of extended thiophloroglucinol ligands and their Ni(II) 3 complexes are evaluated by comparison to their phloroglucinol analogs by means of NMR, FTIR, UV/Vis, and structural parameters. To provide a full set of compounds for this comparison of S versus O substitution, a new triplesalen ligand, its Ni(II) 3 complex, and a new thiophloroglucinol were synthesized. (1) H and (15) N NMR chemical shifts and coupling constants prove that the thiophloroglucinol ligands exist as the N-protonated and not the O-protonated tautomer. (13) C and (15) N NMR chemical shifts and structural parameters further demonstrated that the extended thiophloroglucinol ligands must be described with a predominant thione-enamine (heteroradialene) character despite the participation of a CS double bond. In the Ni(II) 3 complexes, this heteroradialene character is reduced but still predominant.

Synthesis, spectroscopic and conformational analysis of 1,4-dihydroisonicotinic acid derivatives

Structural and conformational properties of 1,4-dihydroisonicotinic acid derivatives, characterized by ester, ketone or cyano functions at positions 3 and 5 in solid and liquid states have been investigated by X-ray analysis and nuclear magnetic resonance and supported by quantum chemical calculations. The dihydropyridine ring in each of the compounds exists in flattened boat-type conformation. The observed ring distortions around the C(4) and N(1) atoms are interrelated. The substituent at N(1) has great influence on nitrogen atom pyramidality. The 1H, 13C and 15N NMR chemical shifts and coupling constants are discussed in terms of their relationship to structural features such as character and position of the substituent in heterocycle, N-alkyl substitution and nitrogen lone pair delocalization within the conjugated system.

Microsolvation, aggregation, and pseudomonomolecular, ionic sp2-stereoinversion mechanism of two exocyclic β,β-di-tert-alkyl-α-arylvinyllithiums

A THF-solvated, crystalline, exocyclic alkenyllithium, (tert-alkyl)2CC(Li)–Ph, was synthesized and shown to be a disolvated dimer in the solid state and in toluene as the solvent; increasing amounts of the monomeric species emerged on cooling the toluene solution. In THF as the solvent, only the trisolvated monomer was present and identified as a contact ion pair (CIP) through its scalar 13C,6Li NMR coupling. This ground-state needs only one further THF ligand as a catalyst for breaking the C–Li bond with formation of a tetrasolvated, solvent-separated ion pair (SSIP) on the way to the transition state of cis/trans sp2-stereoinversion. The ensuing pseudomonomolecular, ionic mechanism is confirmed by low pseudoactivation parameters: enthalpy ΔHψ‡ = 6.9(3) kcal mol−1; entropy ΔSψ‡ = −23.3(9) cal mol−1 K−1. Similar parameters were found with 2,6-dimethylphenyl in place of Ph.

1H and 13C NMR scaling factors for the calculation of chemical shifts in commonly used solvents using density functional theory.

Calculation of NMR chemical shifts and coupling constants using quantum mechanical calculations [density functional theory (DFT)], has become a very popular tool for the determination of conformation and the assignment of stereochemistry within a molecule. We present the scaling factors (linear regression parameters) from 10 DFT methods for 10 commonly used NMR solvents using the same set of reference compounds. The results were compared with the corresponding gas-phase calculations to assess the inclusion of the polarizable continuum model for solvent effects.

Highly syn selective addition of aqueous HBr to hydrophobically shielded arylalkynes

Hydrophobically shielded alkynes HCC–aryl, carrying 2,6-di- and 2,4,6-tri-tert-butylphenyl as the aryl group, can add aqueous HBr on heating in moist chloroform solutions to produce pure H2CC(–Br)–aryl (isolated yields 96%, no hydrolysis). Employment of DCC–aryl furnished initially only the E stereoisomer of DHCC(–Br)–aryl (stereospecific syn addition), which was slowly both dedeuteriated and partially transformed to the Z stereoisomer by HBr. The strongly retarded HBr addition to H3C–CC–aryl in moist chloroform produced again more E than Z product, whereas a thermodynamic E/Z ratio of 10:87 was found in moist acetic acid. Substitution of Br by LiSnMe3 produced H2CC(–SnMe3)–aryl with well resolved long range 119Sn NMR coupling constants.

Conformational analysis of 2,2-difluoroethylamine hydrochloride: double gauche effect.

The gauche effect in fluorinated alkylammonium salts is well known and attributed either to an intramolecular hydrogen bond or to an electrostatic attraction between the positively charged nitrogen and the vicinal electronegative fluorine atom. This work reports the effect of adding a fluorine atom in 2-fluoroethylamine hydrochloride on the conformational isomerism of the resulting 2,2-difluoroethylamine chloride (2). The analysis was carried out using NMR coupling constants in D2O solution, in order to mimic the equilibrium conditions in a physiological medium, in the gas phase and in implicit water through theoretical calculations. Despite the presence of σCH→σ*CF and σCH→σ*CN interactions, which usually rule the hyperconjugative gauche effect in 1,2-disubstituted ethanes, the most important forces leading to the double gauche effect (+NH3 in the gauche relationship with both fluorine atoms) in 2 are the Lewis-type ones. Particularly, electrostatic interactions are operative even in water solution, where they should be significantly attenuated, whereas hyperconjugation and hydrogen bond have secondary importance.

Synthesis and Elaboration of All‐cis‐1,2,4,5‐Tetrafluoro‐3‐Phenylcyclohexane: A Polar Cyclohexane Motif

A stereocontrolled synthesis of all-cis-1,2,4,5- tetrafluoro-3-phenylcyclohexane is developed as the first functionalised example of this polar cyclohexane motif. The dipolar nature of the ring, arising due to two 1,3-diaxial C-F bonds, is revealed in the solid-state (X-ray) structure. The orthogonal conformation of the aryl and cyclohexyl rings in all-cis-1,2,4,5-tetrafluoro-3-phenylcyclohexane, and in an ortho-nitro derivative, result in intramolecular (1h)JHF and (2h)JCF NMR couplings relayed through hydrogen bonding. The aryl group of all-cis-1,2,4,5-tetrafluoro-3-phenylcyclohexane is elaborated in different ways to demonstrate the versatility of this compound for delivering the motif to a range of molecular building blocks.

NMR-Based Explicit Ensemble Dynamics Simulations of Membrane Protein

Various NMR observables, such as chemical shift anisotropy (CSA) and dipolar coupling (DC) in solid-state NMR, and residual dipolar coupling (RDC) in solution NMR experiments, have been used to characterize membrane protein structures. As time- and ensemble-averaged measurements, those observables also embed protein dynamics, which provides collective motions relevant to protein function. However, most of present NMR structure determination approaches do not consider protein-lipid interactions, which are essential determinants of membrane protein structure and function. To overcome these limitations, various NMR observables were utilized as restraints in ensemble dynamics molecular dynamics simulations to investigate protein dynamics in the explicit membranes. As representative membrane proteins, Pf1 coat protein and Fd coat protein were used to set up two model systems separately. Both of them are single-pass transmembrane helical proteins involving one membrane associated periplasmic helix. The resulting structures satisfy the NMR observables and are compared with the published structures. The disposition of protein TM helix in the explicit membrane is identified and the degree of freedom of the helix orientation under NMR restraints is observed.

NaRb7(Si4–xGex)2 – Soluble Zintl Phases Containing Heteroatomic Tetrahedral ­[Si4–xGex]4– Clusters

AbstractThe quaternary phases NaRb7(Si4–xGex)2 (x = 1–3) crystallize with an NaRb7Ge8‐type structure and contain tetrahedral four‐atom clusters that consist of Si and Ge atoms. The quaternary phases possess larger cell volumes with increasing Ge amount. The formation of heteroatomic [Si4–xGex]4– clusters is indicated by chemically different Si environments, which were analyzed by means of solid‐state 29Si MAS (magic‐angle spinning) NMR spectroscopy of a 29Si‐enriched NaRb7(Si4–xGex)2 sample with x = 0.5 as well as quantum chemical calculations of the NMR coupling parameters. NaRb7(Si4–xGex)2 represents another rare example of a phase with exclusively tetrahedral clusters that readily dissolves in liquid ammonia. The nature of the heteroatomic clusters was further investigated by dissolution of NaRb7(Si4–xGex)2 with x = 2 in liquid ammonia. In the presence of MesCu (Mes = mesityl) and 18‐crown‐6 as a sequestering agent, crystals with the composition [Rb(18‐crown‐6)]2Rb2[(MesCu)2(Si4–xGex)](NH3)11 were isolated with x = 2.2(1). [(MesCu)2(Si4–xGex)]4– represents another isomer of a MesCu‐stabilized tetrahedral anion and supports the observation that Zintl phases, which contain solely tetrahedranide subunits, represent a new class of soluble Zintl phases.

Diels–Alder reaction of β-chloro-α,β-unsaturated aldehydes with cyclopentadiene: an experimental and theoretical study

The Diels–Alder cycloaddition reactions of four β-chloro-α,β-unsaturated aldehydes 1–4 with cyclopentadiene were carried out. Only two of these aldehydes (3 and 4) were reactive and afforded highly functionalized norbornene isomers 5–10 in good yields. The Z-ethyl-2-chloro-3-formylacrylate 3 gave two diastereomers endo(COOEt)–exo(CHO) 5 and exo(COOEt)–endo(CHO) 6, whereas a mixture of Z and E of ethyl 3-chloro-2-formyl-4,4,4-trifluorobut-2-enoate 4 afforded the four diastereomers 7–10. These new cycloadducts (CAs) were characterized by NMR, IR, and mass spectrometry. Structural assignments for different isomers were made on the basis of NMR chemical shifts and coupling constants using 1D, 2D, and heteroNOE NMR techniques. A density functional theoretical study on reactants, transition state structures, and CAs was also undertaken in order to support the experimental data.

Relative Configuration of the Marine Natural Product Elatenyne using NMR Spectroscopic and Chemical Derivatization Methodologies

NMR spectroscopic methodologies used to characterize and elucidate the structure of the marine natural product elatenyne were also applied to the characterization of a new triazole structural derivative of elatenyne, obtained by “Click” chemistry. The two most probable relative configurations assigned to naturally occurring elatenyne were concluded on the basis of key single irradiation nOe NMR enhancements, in combination with the use of a variant of the HSQC NMR experiment that permitted NMR coupling constants to be measured for the overlapped ring junction protons. This study represents the first application of “Click” chemistry to chemically derivatize an unmodified natural product.

Characterization by NMR of reactants and products of hydrofluoroether isomers, CF3(CF2)3OCH3 and (CF3)2C(F)CF2OCH3, reacting with isopropyl alcohol

The 3M Company product Novec™ 71IPA DL, a mixture of methoxyperfluorobutane, methoxyperfluoroisobutane and 4.5 wt.% isopropyl alcohol, has been found to be very stable at ambient temperature, producing fluoride at the rate of ~1 ppm/year. Our earlier kinetic and theoretical studies have identified the reaction mechanism. This paper identifies the (1)H and (19)F NMR chemical shifts, multiplicities, and coupling constants of reactants and the major products that result from aging the mixture in sealed Pyrex NMR tubes for periods up to 1.8 years at temperatures from 26 °C to 102 °C. Chemical shifts and coupling constants of fluorine and hydrogen atoms on the hydrofluoroethers and isopropyl alcohol are traced through the reactions to their values in the products--esters, isopropylmethyl ether, and HF. These spectral positions, multiplicities, and coupling constants are presented in table format and as figures to clarify the transformations observed as the samples age.

15N NMR of 1,4‐dihydropyridine derivatives

In this article, we describe the characteristic (15)N and (1)HN NMR chemical shifts and (1)J((15)N-(1)H) coupling constants of various symmetrically and unsymmetrically substituted 1,4-dihydropyridine derivatives. The NMR chemical shifts and coupling constants are discussed in terms of their relationship to structural features such as character and position of the substituent in heterocycle, N-alkyl substitution, nitrogen lone pair delocalization within the conjugated system, and steric effects.

Stereochemistries of monapinones produced by Talaromyces pinophilus FKI-3864

Monapinones A (1) to E (5), half parts of dinapinones, were produced by fermentation of Talaromyces pinophilus FKI-3864 in seawater-containing medium and have a common dihydronaphthopyranone skeleton with a different long alkyl chain. The relative stereochemistries of 3–5 were elucidated by various NMR experiments including analysis of 1H NMR coupling constants, ROESY and the dihedral angles. The absolute stereochemistries of 3–5 at C-3 were determined by the circular dichroism spectra in comparison to the data of (R)- and (S)-semivioxanthins (6 and 7). Accordingly, total absolute stereochemistries of 3–5 were concluded to be 3S,13R,15R,17R,19R,3S,13R,15R,17R and 3S,13R,15R, respectively.

Online ThFFF–NMR: A Novel Tool for Molar Mass and Chemical Composition Analysis of Complex Macromolecules

For the first time, thermal field flow fractionation (ThFFF) was coupled online with 1H NMR. ThFFF is one of the most important separation techniques for the analysis of large complex molecules and molecular assemblies. It provides information on molecular size and chemical composition in cases where multidetector setups are used. Multiple detection, however, is very complex. Using 1H NMR as the sole detector offers a number of significant benefits. First, NMR replaces the need to use multidetector setups. Second, the structure and the microstructure of the molecules as well as the chemical composition of the molecules can be recorded. As the consequence, selective and quantitative information can be directly obtained from the NMR chromatograms. Third, the molar mass distributions of all separated species can be derived directly from these NMR chromatograms. The new online ThFFF–NMR coupling was successfully applied to homopolymers and block copolymers of different molar masses and chemical compositions.

Disorder and order in unfolded and disordered peptides and proteins: A view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β‐type like turn conformations

In the preceding paper, we found that ensembles of tripeptides with long or bulky chains can include up to 20% of various turns. Here, we determine the structural and thermodynamic characteristics of GxG peptides with short polar and/or ionizable central residues (D, N, C), whose conformational distributions exhibit higher than average percentage (>20%) of turn conformations. To probe the side-chain conformations of these peptides, we determined the (3)J(H(α),H(β)) coupling constants and derived the population of three rotamers with χ1 -angles of -60°, 180° and 60°, which were correlated with residue propensities by DFT-calculations. For protonated GDG, the rotamer distribution provides additional evidence for asx-turns. A comparison of vibrational spectra and NMR coupling constants of protonated GDG, ionized GDG, and the protonated aspartic acid dipeptide revealed that side chain protonation increases the pPII content at the expense of turn populations. The charged terminal groups, however, have negligible influence on the conformational properties of the central residue. Like protonated GDG, cationic GCG samples asx-turns to a significant extent. The temperature dependence of the UVCD spectra and (3)J(H(N)H(α)) constants suggest that the turn populations of GDG and GNG are practically temperature-independent, indicating enthalpic and entropic stabilization. The temperature-independent J-coupling and UVCD spectra of GNG require a three-state model. Our results indicate that short side chains with hydrogen bonding capability in GxG segments of proteins may serve as hinge regions for establishing compact structures of unfolded proteins and peptides.

NMR‐based conformational analysis of perezone and analogues

Complete assignment of the (1)H NMR chemical shift and coupling constant values of perezone (1), O-methylperezone (2) and 6-hydroxyperezone (3) was carried out by total-line-shape-fitting calculations using the PERCH iterative spectra analysis software (PERCH Solutions Ltd., Kuopio, Finland). The resulting simulated spectra for the three compounds showed strong similarity to their corresponding experimental spectra. Particularly, all vicinal, allylic and homoallylic coupling constant values for the side chain of the three compounds were very similar, thus revealing that the conformation of these three molecules in solution is indeed almost identical. This fact is in agreement with extended side chain conformations over folded chain conformations because 1, 2 and 3 undergo completely different intramolecular cycloaddition reactions. In addition, results of double pulsed field gradient spin echo NOESY 1D experiments performed on perezone (1) were unable to provide evidence for folded conformers.