Dynamic NMR Studies Research Articles

Competition between Bailar and Ray-Dutt paths in conformational interconversion of tris-chelated complexes: a DFT study

Tris-chelated complexes of aluminum with α-isopropenyltropolonate and α-isopropyltropolonate ligands can be considered prototypical complexes for the study of internal rearrangements through prismatic transient structures. Such isomerization paths, known as Bailar and Ray-Dutt twists, have been suggested for these compounds on the basis of dynamic NMR study, but modern computational methodologies have never been applied to corroborate this finding. In this paper, we report a computational investigation about the internal isomerization processes of the mentioned complexes. Both the Bailar and Ray-Dutt twists have been found as possible reaction paths. The prismatic structures along each reaction path have been described as transition structures rather than intermediate and have been computationally characterized. A comparison between experimental and computational kinetic data has been performed.

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops

In a combined NMR/MD study, the temperature-dependent changes in the conformation of two members of the RNA YNMG-tetraloop motif (cUUCGg and uCACGg) have been investigated at temperatures of 298, 317 and 325 K. The two members have considerable different thermal stability and biological functions. In order to address these differences, the combined NMR/MD study was performed. The large temperature range represents a challenge for both, NMR relaxation analysis (consistent choice of effective bond length and CSA parameter) and all-atom MD simulation with explicit solvent (necessity to rescale the temperature). A convincing agreement of experiment and theory is found. Employing a principle component analysis of the MD trajectories, the conformational distribution of both hairpins at various temperatures is investigated. The ground state conformation and dynamics of the two tetraloops are indeed found to be very similar. Furthermore, both systems are initially destabilized by a loss of the stacking interactions between the first and the third nucleobase in the loop region. While the global fold is still preserved, this initiation of unfolding is already observed at 317 K for the uCACGg hairpin but at a significantly higher temperature for the cUUCGg hairpin.

Dynamic NMR study of the oxaphosphetane complexation with lithium during the Wittig reaction

AbstractDynamic NMR spectroscopy at very low temperatures (148–182 K) reveal the dynamic behavior of the (2‐tri(3‐furyl)‐3‐methyl‐4‐cyclopropenyl‐oxaphosphetane) generated during a Wittig reaction between tri(3‐furyl)ethylphosphonium iodine and cyclopropylaldehyde. The possibility of formation of different adducts between Li+ ions and oxaphosphetane or betainic intermediates was checked calculating the formation enthalpies using the MNDO, AM1, and PM3 semiempirical MO methods. The observed species are interpreted as oxaphosphetane complexes with lithium ions present in solution. Quantum mechanical calculations confirm the spectroscopic results. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Coupling of CpCr(CO)3and Heterocyclic Dithiadiazolyl Radicals. Synthetic, X-ray Diffraction, Dynamic NMR, EPR, CV, and DFT Studies

The reaction of the 1,2,3,5-dithiadiazolyls (4-R-C(6)H(4)CN(2)S(2))(2) (R = Me, 2a; Cl, 2b; OMe, 2c; and CF3, 2d) and (3-NC-5-tBu-C(6)H(3)CN(2)S(2))(2) (2e) with [CpCr(CO)(3)](2) (Cp = eta(5)-C(5)H(5)) (1) at ambient temperature respectively yielded the complexes CpCr(CO)(2)(eta(2)-S(2)N(2)CC(6)H(4)R) (R = 4-Me, 3a; 4-Cl, 3b; 4-OMe, 3c; and 4-CF(3), 3d) and CpCr(CO)(2)(eta(2)-S(2)N(2)CC(6)H(3)-3-(CN)-5-(tBu)) (3e) in 35-72% yields. The complexes 3c and 3d were also synthesized via a salt metathesis method from the reaction of NaCpCr(CO)(3) (1B) and the 1,2,3,5-dithiadiazolium chlorides 4-R-C(60H(4)CN(2)S(2)Cl (R = OMe, 8c; CF(3), 8d) with much lower yields of 6 and 20%, respectively. The complexes were characterized spectroscopically and also by single-crystal X-ray diffraction analysis. Cyclic voltammetry experiments were conducted on 3a-e, EPR spectra were obtained of one-electron-reduced forms of 3a-e, and variable temperature 1H NMR studies were carried out on complex 3d. Hybrid DFT calculations were performed on the model system [CpCr(CO)(2)S(2)N(2)CH] and comparisons are made with the reported CpCr(CO)(2)(pi-allyl) complexes.

Solution Structures of Cyclosporin A and Its Complex with Dysprosium(III) in SDS Micelles: NMR and Molecular Dynamics Studies

Cyclosporin A (CsA) is a cyclic naturally occurring peptide used to prevent graft rejection in organ transplantations. Its immunosuppressive activity is due to the formation of a complex with cyclophilin A (Cyp), in which the cis 9MeLeu-10MeLeu amide bond of CsA assumes a trans conformation. The mechanism of the conformational inversion has not been delineated, but it has been postulated that metal ions binding induces a conformational change that enables CsA to bind Cyp. In this work, we solved the structures of CsA in sodium dodecyl sulfate (SDS) micelles (which enhance its solubility and mimic the hydrophobic environment clinically used for drug delivery) and its complex with Dy(III) ion, whose coordination chemistry is frequently used to reproduce the effect of Ca(II). The paramagnetic properties of Dy(III) allowed us to build up a structure using proton relaxation enhancements, which remains stable in a MD simulation in the micelle environment.

Synthesis and conformational behaviour of lower-rim tetraacetylated thiacalix[4]arenes

The acylation of thiacalix[4]arenes with AcCl or Ac 2O gave the corresponding lower-rim tetraacetoxy derivatives. In contrast to classical calix[4]arenes, tetraacetylated thiacalix[4]arenes are conformationally mobile in solution and represent a thermodynamic equilibrium of three different conformers at room temperature. As proven by a dynamic 1H NMR study, conformational preferences of acetylated thiacalix[4]arenes considerably depend on the upper-rim substitution. Hence, t-Bu thiacalixarene prefers 1, 3- alternate and 1, 2- alternate conformations (43% and 38%, respectively), while the upper-rim unsubstituted compound adopts preferably the partial cone conformation (70%).

Extraction of Hydrophobic Species into a Water-Soluble Synthetic Receptor

A deep, water-soluble cavitand extracts a variety of neutral hydrophobic species into its cavity. Flexible species such as n-alkanes tumble rapidly on the NMR time scale inside the cavity, but this motion is slowed for bulkier guests. Long, rigid guests such as p-substituted aromatics are either static or only tumble at elevated temperatures via flexing motions of the cavitand. Strong selectivity in recognition of long rigid guests is seen. The binding of neutral guests occurs via the classical hydrophobic effect; the process is entropically favored, as shown by isothermal titration calorimetry measurements. Binding affinities are generally on the order of 10(4)-10(5) M(-1). The extent of the hydrophobic stabilization is shown by the binding of long trimethylammonium salts, which bind the alkyl chain in the cavity, rather than the NMe3+ group. Dynamic NMR studies show that self-exchange of neutral guests is independent of guest concentration, and most likely occurs via rate-determining unfolding of the cavitand. In the absence of guests, the cavitand exists in a dimeric velcrand structure.

Computational and experimental studies of the conformational reactions of 1,3,5-tris(pentaphenylphenyl)benzene

Computational analyses of the five possible functional group rotations in 1,3,5-tris(pentaphenylphenyl)benzene ( 1) were conducted at three disparate levels of theory: AM1, HF/STO-3G, and B3LYP/6-31G(d). The ground state and transition state structures were located for all of the conformational reactions, and the free energies of activation for these processes were calculated. In addition, compound 1 was resolved by low-temperature chromatography on a chiral support, and its barrier to racemization was determined by dynamic chromatography. These computational and experimental results are compared with data from dynamic NMR studies of 1 in the literature.

In situ high temperature 27Al NMR study of structure and dynamics in a calcium aluminosilicate glass and melt

The temperature dependence (25–1400 °C) of 27Al NMR spectra and spin–lattice relaxation time constants T 1 have been studied for a calcium aluminosilicate (43.1CaO–12.5Al 2O 3–44.4SiO 2) glass and melt using an in situ high temperature probe, and the glass has been characterized by ambient temperature, high field MAS NMR. The peak positions and the line widths show a consistent behavior as motional averaging of the quadrupolar satellites increases with increasing temperature. The rate of decrease with temperature of T 1 drastically increases near the glass transition temperature T g, which suggests a change in NMR relaxation process from vibrational to translational motions. Above the T 1 minimum (≈1200 °C), NMR correlation times obtained from T 1 are in good agreement with shear relaxation times estimated from viscosity, suggesting that microscopic nuclear spin relaxation is controlled by the same dynamics as macroscopic structural relaxation, and thus that atomic-scale motion is closely related to macroscopic viscous flow.

Review NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings

An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, and RNA synthesis itself. The measurement of NMR residual dipolar couplings (RDCs) in partially aligned systems is providing new insights into the structural plasticity of RNA through combined characterization of large-amplitude collective helix motions and local flexibility in noncanonical regions over a wide window of biologically relevant timescales (<milliseconds). Here, we review RDC methodology for studying RNA structural dynamics and survey what has been learnt thus far from application of these methods. Future methodological challenges are also identified.

3D-Structure of the interior fusion peptide of HGV/GBV-C by 1H NMR, CD and molecular dynamics studies

In this work, we present a structural characterization of the putative fusion peptide E2(279–298) corresponding to the E2 envelope protein of the HGV/GBV-C virus by 1H NMR, CD and MD studies performed in H 2O/TFE and in lipid model membranes. The peptide is largely unstructured in water, whereas in H 2O/TFE and in model membranes it adopts an helical structure (approximately 65–70%). The partitioning free energy Δ G ranges from −6 to −7.5 kcal mol −1. OCD measurements on peptide-containing hydrated and oriented lipid multilayers showed that the peptide adopts a predominantly surface orientation. The 1H NMR data (observed NOEs, deuterium exchange rates, Hα chemical shift index and vicinal coupling constants) and the molecular dynamics calculations support the conclusions that the peptide adopts a stable helix in the C-terminal 9–18 residues slightly inserted into the lipid bilayer and a major mobility in the amino terminus of the sequence (1–8 residues).

A Comparative NMR Study of the Polypeptide Backbone Dynamics of Hemoglobin in the Deoxy and Carbonmonoxy Forms

Model-free-based NMR dynamics studies have been undertaken for polypeptide backbone amide N-H bond vectors for both the deoxy and carbonmonoxy forms of chain-specific, isotopically (15N and 2H) labeled tetrameric hemoglobin (Hb) using 15N-relaxation parameters [longitudinal relaxation rate (R1), transverse relaxation rate (R2), and heteronuclear nuclear Overhauser effect (NOE)] measured at two temperatures (29 and 34 degrees C) and two magnetic field strengths (11.7 and 14.1 T). In both deoxy and carbonmonoxy forms of human normal adult hemoglobin (Hb A), the amide N-H bonds of most amino acid residues are rigid on the fast time scale (nanosecond to picosecond), except for the loop regions and certain helix-helix connections. Although rigid in deoxy-Hb A, beta146His has been found to be free from restriction of its backbone motions in the CO form, presumably due to the rupture of its hydrogen bond/salt bridge network. We now have direct dynamics evidence for this structural transition of Hb in solution. While remarkably flexible in the deoxy state, alpha31Arg and beta123Thr, neighbors in the intradimer (alpha1beta1) interface, exhibit stiffening upon CO binding. These findings imply a role for alpha31Arg and beta123Thr in the intradimer communication but contradict the results from X-ray crystallography. We have also found that there is considerable flexibility in the intradimer (alpha1beta1) interface (i.e., B, G, and H helices and the GH corner) and possible involvement of several amino acid residues (e.g., alpha31Arg, beta3Leu, beta41Phe, beta123Thr, and beta146His) in the allosteric pathway. Several amino acid residues at the intradimer interfaces, such as beta109Val, appear to be involved in possible conformational exchange processes. The dynamic picture derived from the present study provides new insights into the traditional description of the stereochemical mechanism for the cooperative oxygenation of Hb A based on X-ray crystallographic results.

A Solid-State NMR Study of Hydrogen-Bonding Networks and Ion Dynamics in Benzimidazole Salts

On the basis of our solid-state NMR characterization of dynamics in two model salts, we draw the analogy to the fuel cell membrane candidate, phosphoric acid-doped poly(benzimidazole), and conclude that phosphate anion dynamics contribute to long-range proton transport, whereas the mobility of the polymer itself is not a contributing factor. This is contrasted with emerging membrane candidates, which rely on fully covalently bonded acid donors and acceptors, and target high-temperature PEM fuel cell operation in the absence of liquid electrolyte. The hydrogen-bonding structures of benzimidazolium phosphate and benzimidazolium methane phosphonate are established using X-ray diffraction paired with solid-state 1H DQF NMR. By comparing the dynamics of the phosphate and methane phosphonate anions with the dynamics of imidazolium and benzimidazolium cations, the relative importance of these processes in proton transport is determined. The imidazolium cation is known to undergo two-site ring reorientation on the millisecond time scale. In contrast, it is shown here that the benzimidazolium rings are immobile in analogous salts, on a time scale extending into the tens of seconds. Therefore, we look to the phosphate anions and demonstrate that the time scale of tetrahedral reorientation is comparably fast (50 ms). Moreover, the 31P CODEX NMR data clearly indicate a four-site jump process. In contrast, the methane phosphonate undergoes a three-site jump on a slower time scale (75 ms). A mechanism for a zigzag pathway of proton transport through the phosphonate salt crystallites is developed based on the 31P CODEX and 1H variable-temperature MAS NMR data.

Synthesis and dynamic NMR studies of Pt(η 5-C 5Me 5)(CO){C(O)NR 2} complexes

The formation of Pt(η 5-C 5Me 5)(CO){C(O)NR 2} (R = Me, Et) complexes was established by spectroscopic analysis. The infrared spectra of these complexes showed a sharp absorption due to the presence of coordinated carbonyl group in the region 2017–2013 cm −1. The N, N-dialkylcarbamoyl ligands showed a characteristic C O stretching absorption in the range 1609–1616 cm −1. The proton NMR spectra of these complexes revealed the expected singlet arising from five equivalent methyl groups on the cyclopentadienyl ring with satellites due to coupling to 195Pt. The N-methyl and N-ethyl protons exhibited very broad resonances due to restricted rotation about the N–C bond at room temperature. On cooling to −30 °C, the N, N-dimethyl protons for complex Pt(η 5-C 5Me 5)(CO){C(O)NMe 2} showed two sharp singlets at δ 2.86 and 3.09 ppm as expected for the static structure. For the N, N-diethyl derivative, Pt(η 5-C 5Me 5)(CO){C(O)NEt 2}, the methyl protons exhibited only a single triplet at δ 1.06 ppm at −10 °C due to coupling with the methylene protons. This single resonance arises through accidental overlap as the methylene protons of the ethyl groups are inequivalent at this temperature and each exhibited a quartet at δ 3.33 and 3.70 ppm due to coupling with the methyl protons. The singlet resonances for the methyl and ring carbons of the η 5-C 5Me 5 group found in 13C{ 1H} NMR spectra are illustrative of the chemical equivalence of all the carbon atoms caused by free rotation of the ring in these complexes. The signals attributable to the carbonyl and carbamoyl carbon atom resonances are found downfield as two singlets each with a large coupling constant to platinum. The platinum coupling constants of the downfield resonances could not be identified for Pt(η 5-C 5Me 5)(CO){C(O)NMe 2} due to presence of impurities.

Osmium(II) and Ruthenium(II) Arene Maltolato Complexes: Rapid Hydrolysis and Nucleobase Binding

Density functional calculations show that aquation of [Os(eta6-arene)(XY)Cl]n+ complexes is more facile for complexes in which XY=an anionic O,O-chelated ligand compared to a neutral N,N-chelated ligand, and the mechanism more dissociative in character. The O,O-chelated XY=maltolato (mal) [M(eta6-p-cym)(mal)Cl] complexes, in which p-cym=p-cymene, M=OsII (1) and RuII (2), were synthesised and the X-ray crystal structures of 1 and 22 H2O determined. Their hydrolysis rates were rapid (too fast to follow by NMR spectroscopy). The aqua adduct of the OsII complex 1 was 1.6 pKa units more acidic than that of the RuII complex 2. Dynamic NMR studies suggested that O,O-chelate ring opening occurs on a millisecond timescale in coordinating proton-donor solvents, and loss of chelated mal in aqueous solution led to the formation of the hydroxo-bridged dimers [(eta6-p-cym)M(mu-OH)3M(eta6-p-cym)]+. The proportion of this dimer in solutions of the OsII complex 1 increased with dilution and it predominated at micromolar concentrations, even in the presence of 0.1 M NaCl (conditions close to those used for cytotoxicity testing). Although 9-ethylguanine (9-EtG) binds rapidly to Os(II) in 1 and more strongly (log K=4.4) than to RuII in 2 (log K=3.9), the OsII adduct [Os(eta6-p-cym)(mal)(9EtG)]+ was unstable with respect to formation of the hydroxo-bridged dimer at micromolar concentrations. Such insights into the aqueous solution chemistry of metal-arene complexes under biologically relevant conditions will aid the rational design of organometallic anticancer agents.

Dynamic 1H NMR Study of the Barrier to Rotation about the C−N Bond in Primary Carbamates and Its Solvent Dependence

The dynamic 1H NMR study of some primary carbamates in the solvents CDCl3 and CD3COCD3 between 183 and 298 K is reported. The free energies of activation, thus obtained (12.4 to 14.3 kcal mol-1), were attributed to the conformational isomerization about the N-C bond. These barriers to rotation show solvent dependence in contrast to the tertiary analogues and are lower in free energy by ca. 2-3 kcal mol-1.

Automated Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution in Real-Time NMR Spectroscopy

A technique is described that allows reducing acquisition times of multidimensional NMR experiments by extensive spectral folding. The method is simple and has many interesting applications for NMR studies of molecular structure, dynamics, and kinetics.

NMR studies of dynamics in RNA and DNA by 13C relaxation

RNA and DNA molecules experience motions on a wide range of time scales, ranging from rapid localized motions to much slower collective motions of entire helical domains. The many functions of RNA in biology very often require this molecule to change its conformation in response to biological signals in the form of small molecules, proteins or other nucleic acids, whereas local motions in DNA may facilitate protein recognition and allow enzymes acting on DNA to access functional groups on the bases that would otherwise be buried in Watson-Crick base pairs. Although these statements make a compelling case to study the sequence dependent dynamics in nucleic acids, there are few residue-specific studies of nucleic acid dynamics. Fortunately, NMR studies of dynamics of nucleic acids and nucleic acids-protein complexes are gaining increased attention. The aim of this review is to provide an update of the recent progress in studies of nucleic acid dynamics by NMR based on the application of solution relaxation techniques.

Structural, dynamical and functional aspects of the inner motions in the blue copper protein azurin

Molecular dynamics was applied to dissect out the internal motions of azurin, a copper protein performing electron transfer. Simulations of 16.5 ns were analyzed in search of coordinated displacements of amino acid residues that are important for the protein function. A region with high conformational instability was found in the ‘southern’ end of the molecule, far away from the copper site and the binding sites for the redox partners of azurin. By excluding the ‘southern’ region from the subsequent analysis, correlated motions were identified in the hydrophobic patch that surrounds the protein active site. The simulation results are in excellent agreement with recent NMR data on azurin in solution [A. V. Zhuravleva, D. M. Korzhnev, E. Kupce, A. S. Arseniev, M. Billeter, V. Y. Orekhov, Gated electron transfers and electron pathways in azurin: a NMR dynamic study at multiple fields and temperatures, J. Mol. Biol. 342 (2004) 1599–1611] and suggest a rationale for cooperative displacements of protein residues that are thought to be critical for the electron transfer process. A number of other structural and dynamic features of azurin are discussed in the context of the blue copper protein family and an explanation is proposed to account for the variability/conservation of some regions in the cupredoxins.

1H NMR study of proton dynamics in (NH 4) 3H(SO 4) 2

Proton dynamics in (NH 4) 3H(SO 4) 2 has been studied by means of 1H solid-state NMR. The 1H magic-angle-spinning (MAS) NMR spectra were traced at room temperature (RT) and at Larmor frequency of 400.13 MHz. 1H static NMR spectra were measured at 200.13 MHz in the range of 135–490 K. 1H spin-lattice relaxation times, T 1, were measured at 200.13 and 19.65 MHz in the ranges of 135–490 and 153–456 K, respectively. The 1H chemical shift for the acidic proton (14.7 ppm) indicates strong hydrogen bonds. In phase III, NH 4 + reorientation takes place; one type of NH 4 + ions reorients with an activation energy ( E a) of 14 kJ mol − 1 and the inverse of a frequency factor ( τ 0) of 0.85 × 10 − 14 s. In phase II, a very fast local and anisotropic motion of the acidic protons takes place. NH 4 + ions start to diffuse translationally, and no proton exchange is observed between NH 4 + ions and the acidic protons. In phase I, both NH 4 + ions and the acidic protons diffuse translationally. The acidic protons diffuse with parameters of E a = 27 kJ mol − 1 and τ 0 = 4.2 × 10 − 13 s. The translational diffusion of the acidic protons is responsible for the macroscopic proton conductivity, as the NH 4 + translational diffusion is slow and proton exchange between NH 4 + ions and the acidic protons is negligible.