High-pressure NMR Spectroscopy Research Articles

Quantitative composition analysis of natural gas by high-pressure proton low-field NMR spectroscopy: Development of an improved experimental methodology

Natural gas (NG) has been proposed as a bridging fuel between fossil and renewable energy sources, playing a significant role in the decarbonization of the energy sector. Its commercial value and the integrity of the NG infrastructure depend on the NG physical properties, which are strongly related to its composition. Thus, the development of low-cost and reliable analytical methods for composition analysis of NG can enable a more efficient operation. Recently, we showed that high-pressure (HP) benchtop 1H NMR spectroscopy combined with indirect hard modelling (IHM) is an efficient and low-cost method for composition quantification of NG. The current work extends this methodology by introducing and testing novel experimental strategies for increasing the reliability and accuracy of the method. This new approach includes the use of a recently published high-pressure tube design and single-scan acquisition combined with novel quality control parameters to obtain highly reproducible peak shape 1H NMR spectra over long periods. The proposed methodology tested on binary, ternary, and more complex mixtures at 200 bar and 160 bar gives compositions in excellent agreement with the vendor certificates.

Including the Ensemble of Unstructured Conformations in the Analysis of Protein's Native State by High-Pressure NMR Spectroscopy.

The analysis of pressure induced changes in the chemical shift of proteins allows statements on structural fluctuations proteins exhibit at ambient pressure. The inherent issue of separating general pressure effects from structural related effects on the pressure dependence of chemical shifts has so far been addressed by considering the characteristics of random coil peptides on increasing pressure. In this work, chemically and pressure denatured states of the cold shock protein B from Bacillus subtilis (BsCspB) have been assigned in 2D 1H-15N HSQC NMR spectra and their dependence on increasing hydrostatic pressure has been evaluated. The pressure denatured polypeptide chain has been used to separate general from structural related effects on 1H and 15N chemical shifts of native BsCspB and the implications on the interpretation of pressure induced changes in the chemical shift regarding the structure of BsCspB are discussed. It has been found that the ensemble of unstructured conformations of BsCspB shows different responses to increasing pressure than random coil peptides do. Thus, the approach used for considering the general effects that arise when hydrostatic pressure increases changes the structural conclusions that are drawn from high pressure NMR spectroscopic experiments that rely on the analysis of chemical shifts.

Solution structure and pressure response of thioredoxin-1 of Plasmodium falciparum.

We present here the solution structures of the protein thioredoxin-1 from Plasmodium falciparum (PfTrx-1), in its reduced and oxidized forms. They were determined by high-resolution NMR spectroscopy at 293 K on uniformly 13C-, 15N-enriched, matched samples allowing to identification of even small structural differences. PfTrx-1 shows an α/β-fold with a mixed five-stranded β-sheet that is sandwiched between 4 helices in a β1 α1 β2 α2 β3 α3 β4 β5 α4 topology. The redox process of the CGPC motif leads to significant structural changes accompanied by larger chemical shift changes from residue Phe25 to Ile36, Thr70 to Thr74, and Leu88 to Asn91. By high-field high-pressure NMR spectroscopy, rare conformational states can be identified that potentially are functionally important and can be used for targeted drug development. We performed these experiments in the pressure range from 0.1 MPa to 200 MPa. The mean combined, random-coil corrected B1* values of reduced and oxidized thioredoxin are quite similar with -0.145 and -0.114 ppm GPa-1, respectively. The mean combined, random-coil corrected B2* values in the reduced and oxidized form are 0.179 and 0.119 ppm GPa-2, respectively. The mean ratios of the pressure coefficients B2/B1 are -0.484 and -0.831 GPa-1 in the reduced and oxidized form respectively. They differ at some points in the structure after the formation of the disulfide bond between C30 and C33. The thermodynamical description of the pressure dependence of chemical shifts requires the assumption of at least three coexisting conformational states of PfTrx-1. These three conformational states were identified in the reduced as well as in the oxidized form of the protein, therefore, they represent sub-states of the two main oxidation states of PfTrx-1.

Formic acid as the H2-carrier and the transfer hydrogenation reagent for Ru-catalyzed hydroaminomethylation of olefins

Formic acid (FA) is a potential hydrogen storage substance due to its abundant resources, ease of storage, and high hydrogen content. In this paper, the hydroaminomethylation of olefins with FA as the hydrogen source was accomplished over DPEPhos-based Ru catalyst for the first time. Under optimal conditions, α-olefins or cycloolefins with steric hindrance obtained 62%∼96% yields of the target amines. The influence of FA was investigated by in situ high-pressure 1H NMR spectroscopy analyses, isotope labelling experiments, and the separated hydroformylation or reduction amination. It was indicated that FA was decomposed to provide H2 for the hydroformylation, and was used as a reducing agent in the transfer hydrogenation of imines/enamines. The reversible amidation of FA with substrate amine could inhibit the side reaction of aldehydes transfer hydrogenation. Moreover, the involving FA would facilitate the formation of Ru-H species, thereby promoting the hydroaminomethylation.

Defining the role of the N-terminal helix in the Arf1 nucleotide switch transition using pressure perturbation.

ADP-Ribosylation Factors (Arfs) are small GTPases that act as molecular “switches” for the signaling cascades responsible for membrane organization within eukaryotic cells. Overactivation and mutations of Arfs or their binding partners have been implicated in several genetic neurological diseases and breast cancer. Within the Arf family, Arf1 is one of the most studied. In its inactive conformation, the protein is bound to GDP and requires the reorganization of the N-terminal third of the protein to accommodate the dissociation and subsequent bind of GTP. During this conformational change, the myristoylated N-terminal helix becomes disordered allowing Arf1 to associate with membranes. Previous literature suggests that the position of the N-terminal helix is the determinant of the nucleotide exchange. In the Δ17Arf1 mutant, increased structural dynamics is observed and the protein can undergo a switch transition in absence of a membrane. We hypothesize that the N-terminal helix of Arf1 enhances the stability of the GDP bound state of the protein and the nucleotide exchange occurs under stringent control. We used high-pressure 1H-15N HSQC NMR spectroscopy and high-pressure SAXS to investigate the effect of the N-terminal helix for protein stability and the nucleotide switch transition. Further, analysis of the relaxation rates from CPMG and CEST provide greater insight into the structural dynamics of the switch transition. Our data provides evidence that the stability of Arf1 can be attributed in part to the presence of the N-terminal helix.

Surface Interactions and Nanoconfinement of Methane and Methane plus CO2 Revealed by High-Pressure Magic Angle Spinning NMR Spectroscopy and Molecular Dynamics.

This study explores the fundamental, molecular- to microscopic-level behavior of methane gas confined into nanoporous silica proxies with different pore diameters and surface-to-volume (S/V) ratios. Surfaces and pore walls of nanoporous silica matrices are decorated with hydroxyl (-OH) groups, resembling natural heterogeneity. High-pressure MAS NMR was utilized to characterize the interactions between methane and the engineered nanoporous silica proxies under various temperature and pressure regimes. There was a change in the chemical shift position of confined methane slightly in the mixtures with nanoporous silica up to 393 K, as shown by high-pressure 13C-NMR. The 13C-NMR chemical shift of methane was changed by pressure, explained by the densification of methane inside the nanoporous silica materials. The influence of pore diameter and S/V of the nanoporous silica materials on the behaviors and dynamics of methane were studied. The presence of CO2 in mixtures of silica and methane needs analysis with caution because CO2 in a supercritical state and gaseous CO2 change the original structure of nanoporous silica and change surface area and pore volume. According to simulation, the picosecond scale dynamics of methane confined in larger pores of amorphous silica is faster. In the 4 nm pore, the diffusivity obtained from MD simulations in the pore with a higher S/V ratio is slower due to the trapping of methane molecules in adsorbed layers close to the corrugated pore surface. In contrast, relaxation measured with NMR for smaller pores (higher S/V) exhibits larger T1, indicating slower relaxation.

Refined high-pressure tube design for improved resolution in high-pressure NMR spectroscopy.

High-pressure NMR spectroscopy has become a valuable analytical tool in many activities, including the energy sector, chemical research, and biophysics. Many pressure-based applications could benefit from low-field NMR. In this context, a novel, simple, and low-cost high-pressure tube design improving the signal-to-noise ratio by more than 80% is presented.

Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography.

In this work, we experimentally investigate the allosteric transitions between conformational states on the Ras oncogene protein using high pressure crystallography. Ras protein is a small GTPase involved in central regulatory processes occurring in multiple conformational states. Ras acts as a molecular switch between active GTP-bound, and inactive GDP-bound states, controlling essential signal transduction pathways. An allosteric network of interactions between the effector binding regions and the membrane interacting regions is involved in Ras cycling. The conformational states which coexist simultaneously in solution possess higher Gibbs free energy than the ground state. Equilibria between these states can be shifted by applying pressure favouring conformations with lower partial molar volume, and has been previously analyzed by high-pressure NMR spectroscopy. High-pressure macromolecular crystallography (HPMX) is a powerful tool perfectly complementary to high-pressure NMR, allowing characterization at the molecular level with a high resolution the different allosteric states involved in the Ras cycling. We observe a transition above 300 MPa in the crystal leading to more stable conformers. Thus, we compare the crystallographic structures of Ras(wt)·Mg2+·GppNHp and Ras(D33K)·Mg2+·GppNHp at various high hydrostatic pressures. This gives insight into per-residue descriptions of the structural plasticity involved in allosteric equilibria between conformers. We have mapped out at atomic resolution the different segments of Ras protein which remain in the ground-state conformation or undergo structural changes, adopting excited-energy conformations corresponding to transient intermediate states. Such in crystallo phase transitions induced by pressure open the possibility to finely explore the structural determinants related to switching between Ras allosteric sub-states without any mutations nor exogenous partners.

Protein-Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure.

Proteins undergo changes in their partial volumes in numerous biological processes such as enzymatic catalysis, unfolding–refolding, and ligand binding. The change in the protein volume upon ligand binding—a parameter termed the protein–ligand binding volume—can be extensively studied by high-pressure NMR spectroscopy. In this study, we developed a method to determine the protein–ligand binding volume from a single two-dimensional (2D) 1H–15N heteronuclear single quantum coherence (HSQC) spectrum at different pressures, if the exchange between ligand-free and ligand-bound states of a protein is slow in the NMR time-scale. This approach required a significantly lower amount of protein and NMR time to determine the protein–ligand binding volume of two carbonic anhydrase isozymes upon binding their ligands. The proposed method can be used in other protein–ligand systems and expand the knowledge about protein volume changes upon small-molecule binding.

水中におけるナフタレン骨格超分子チューブと1,4-ジオキサンの複合体形成と圧力効果

Host-guest interactions between a pair of naphthalene-based molecular tubes (i.e., anti-isomer and syn-isomer) and 1,4-dioxiane have been studied to understand selective recognition. Volume changes for complexation of the amide naphthotubes with 1,4-dioxane were investigated using high-pressure fluorescence and high-pressure NMR spectroscopy. We found that the partial molar volume change (ΔV°) for the association of 1,4-dioxane with the naphthotubes was －6.3±0.1 mL mol－1 for the anti-isomer and 3.2±0.4 mL mol－1 for the syn-isomer. To elucidate the molecular basis of ΔV°, molecular dynamics simulations of the complexation process were also performed. The difference in ΔV° was attributed to variations in the shape and hydration of naphthotube hydrophobic cavities.

Proton mobility in metallic copper hydride from high-pressure nuclear magnetic resonance

Atomic and electronic structures of Cu2H and CuH have been investigated by high pressure NMR spectroscopy, X-ray diffraction and ab-initio calculations. Metallic Cu2H was synthesized at a pressure of 40 GPa, and semi-metallic CuH at 90 GPa, found stable up to 160 GPa. Experiments and computations suggest the formation of a metallic 1H-sublattice as well as a high 1H mobility of ~10-7 cm2/s in Cu2H. Comparison of Cu2H and FeH data suggests that deviations from Fermi gas behavior, formation of conductive hydrogen networks, and high 1H mobility could be common features of metal hydrides.

A polymeric ionic liquid catalyst for the N-formylation and N-methylation of amines using CO2/PhSiH3

We describe a polymeric ionic liquid (PIL) derived from trimethyl(p-vinylbenzyl)ammonium chloride ([VBTAm]Cl) that efficiently catalyzes the N-formylation of amines employing CO2 and PhSiH3 at room temperature with low catalyst loadings in near-quantitative yield. Under more forcing conditions N-methylated products can be selectively obtained. The PIL catalyst can be easily recovered and reused repeatedly without a decrease in activity. The reaction mechanism was studied in situ using high-pressure NMR spectroscopy and a tentative mechanistic cycle has been proposed.

High-pressure NMR spectroscopy in studies of the conformational composition of small molecules in supercritical carbon dioxide

An experimental approach in conducting NMR measurements at supercritical parameters of state is discussed. A novel design of the high-pressure NMR cell was developed which allowed eliminating the field inhomogeneity and, thus, increasing the sensitivity of the experiment at the supercritical state. Analysis of the MD simulations and NMR data showed that two conformers of ibuprofen dominate in the solution in supercritical CO2 along the critical isochore 1.3 \r{ho}cr(CO2). Conformer populations calculated from MD simulations and from NMR spectra agree with each other

High-temperature, high-pressure hydrothermal synthesis, crystal structure, and infrared and NMR spectroscopy of a barium lead borate with a 2D layer structure: [Ba3Pb(H2O)][B11O19(OH)3

With a high-temperature, high-pressure hydrothermal technique, a new barium lead borate, [Ba3Pb(H2O)][B11O19(OH)3] (1), has been synthesized and characterized by single-crystal X-ray diffraction, and infrared and solid-state NMR spectroscopy. The structure of 1 contains planar thick layers of borates with the Ba2+ cations at sites in the inter- and intralayer space. Each layer consists of three single sheets. The central sheet is very corrugated and is built up from the fundamental building block (FBB) 2Δ3□:Δ2□-Δ2□. On both sides of the central sheet there are borate single chains formed of the very rare FBB 2Δ4□:Δ2□-3□Δ via corner-sharing. This FBB was first observed in a high-pressure polymorph of CaB2O4. These chains are linked into a sheet by PbO5(H2O) polyhedra, which are further linked to the central sheet by sharing vertices between triangles and tetrahedra to form a thick layer. The IR spectrum shows the presence of hydroxyl groups of HBO4, water molecules, BO3 triangles, and BO4 tetrahedra. The presence of BO3 and BO4 polyhedra was also confirmed by 11B MAS NMR spectroscopy.

Recent Developments in the Scope, Practicality, and Mechanistic Understanding of Enantioselective Hydroformylation.

In the nearly 80 years since catalytic hydroformylation was first reported, hundreds of billions of pounds of aldehyde have been produced by this atom efficient one-carbon homologation of alkenes in the presence of H2 and CO. Despite the economy and demonstrated scalability of hydroformylation, the enantioselective process (asymmetric hydroformylation, AHF) currently does not contribute significantly to the production of chiral aldehydes and their derivatives. Current impediments to practical application of AHF include low diversity of chiral ligands that provide effective rates and selectivities, limited exploration of substrate scope, few demonstrations of efficient flow reactor processes, and incomplete mechanistic understanding of the factors that control reaction selectivity and rate. This Account summarizes developments in ligand design, substrate scope, reactor technology, and mechanistic understanding that advance AHF toward practical and atom-efficient production of chiral α-stereogenic aldehydes. Initial applications of AHF were limited to activated terminal alkenes such as styrene, but recent developments enable high selectivity for unactivated olefins and more complex substrates such as 1,1'- and 1,2-disubstituted alkenes. Expanded substrate scope primarily results from new chiral phosphine ligands, especially phospholanes and bisdiazaphospholanes (BDPs). These ligands are now more accessible due to improved synthesis and resolution procedures. One of the virtues of diazaphospholanes is the relative ease of derivatization, including attachment to heterogeneous supports. Hydroformylation involves toxic and flammable reactants, a serious concern in pharmaceutical production facilities. Flow reactors offer many process benefits for handling dangerous reagents and for systematically moving from research to production scales. New approaches to achieving good gas-liquid mixing in flow reactors have been demonstrated with BDP-derived catalyst systems and lend assurance that AHF can be practically implemented by the pharmaceutical and fine chemical industries. To date, progress in AHF has been empirically driven, because hydroformylation is a complex, multistep process for which the origins of chemo-, regio-, and enantioselectivity are difficult to elucidate. Mechanistic complexity arises from three concurrent catalytic cycles (linear and two diastereomeric branched paths), significant pooling of catalyst as off-cycle species, and multiple elementary steps that are kinetically competitive. Addressing such complexity requires new approaches to collecting kinetic and extra-kinetic information and analyzing these data. In this Account, we describe our group's progress toward understanding the complex kinetics and mechanism of AHF as catalyzed by rhodium bis(diazaphospholane) catalysts. Our strategy features both "outside-in" (i.e., monitoring catalytic rates and selectivities as a function of reactant concentration and temperature) and "inside-out" (i.e., building kinetic models based on the rates of component steps of the catalytic reaction) approaches. These studies include isotopic labeling, interception and characterization of catalytic intermediates using NMR techniques, multinuclear high-pressure NMR spectroscopy, and sophisticated kinetic modeling. Such broad-based approaches illuminate the kinetic and mechanistic origins of selectivity and activity of AHF and the elucidation of important principles that apply to all catalytic reactions.

Monitoring Unfolding of Titin I27 Single and Bi Domain with High-Pressure NMR Spectroscopy

A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the folding energy landscape. Simulations, when corroborated by experimental data yielding global information on the folding process, can provide this level of insight. Molecular dynamics (MD) has often been combined with force spectroscopy experiments to decipher the unfolding mechanism of titin immunoglobulin-like single or multidomain, the giant multimodular protein from sarcomeres, yielding information on the sequential events during titin unfolding under stretching. Here, we used high-pressure NMR to monitor the unfolding of titin I27 Ig-like single domain and tandem. Because this method brings residue-specific information on the folding process, it can provide quasiatomic details on this process without the help of MD simulations. Globally, the results of our high-pressure analysis are in agreement with previous results obtained by the combination of experimental measurements and MD simulation and/or protein engineering, although the intermediate folding state caused by the early detachment of the AB β-sheet, often reported in previous works based on MD or force spectroscopy, cannot be detected. On the other hand, the A′G parallel β-sheet of the β-sandwich has been confirmed as the Achilles heel of the three-dimensional scaffold: its disruption yields complete unfolding with very similar characteristics (free energy, unfolding volume, kinetics rate constants) for the two constructs.

Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology.

Pressure and temperature are the two fundamental variables of thermodynamics. Temperature and chemical perturbation are central experimental tools for the exploration of macromolecular structure and dynamics. Though it has long been recognized that hydrostatic pressure offers a complementary and often unique view of macromolecular structure, stability and dynamics, it has not been employed nearly as much. For solution NMR applications the limited use of high-pressure is undoubtedly traced to difficulties of employing pressure in the context of modern multinuclear and multidimensional NMR. Limitations in pressure tolerant NMR sample cells have been overcome and enable detailed studies of macromolecular energy landscapes, hydration, dynamics and function. Here we review the practical considerations for studies of biological macromolecules at elevated pressure, with a particular emphasis on applications in protein biophysics and structural biology.

High Hydrostatic Pressure (HHP), Xenon as a Probe and spin Labelling of the N-Terminal Domain Reveal a Whole Variety of Conformational Transitions in the Full-Length Human Prion Protein

Transmissible spongiform encephalopathies (TSEs) are a group of fatal neurodegenerative disorders associated with the accumulation of fibrils of misfolded prion protein PrP. Conformational intermediates of the human prion protein huPRPc were characterized by a combination of either high hydrostatic pressure (up to 200 MPa) as well as xenon gas pressure and spin labelling experiments at positons 93 or 107 with two-dimensional [1H, 15N]-HSQC NMR spectroscopy. Xenon binds to four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23-230). A fifth xenon binding site is formed transiently by amino acids A120 to L125 of the N-terminal domain and by amino acids K185 to T193 of the core. A model including a dynamic opening and closing of the cavities allowed to derive the individual microscopic and macroscopic dissociation constants. A structural coupling between the N-terminal domain and the core domain can now be confirmed by high pressure NMR spectroscopy, xenon binding and spin labelling experiments.

Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin.

Rational mutation of proteins based on their structural and dynamic characteristics is a useful strategy for amplifying specific fluctuations in proteins. Here, we show the effects of mutation on the conformational fluctuations and thermodynamic stability of ubiquitin. In particular, we focus on the salt bridge between K11 and E34 and the hydrogen bond between I36 and Q41, which are predicted to control the fluctuation between the basic folded state, N1, and the alternatively folded state, N2, of the protein, using high-pressure NMR spectroscopy. The E34A mutation, which disrupts the salt bridge, did not alter picosecond–to–nanosecond, microsecond–to–millisecond dynamic motions, and stability of the protein, while the Q41N mutation, which destabilizes the hydrogen bond, specifically amplified the N1–N2 conformational fluctuation and decreased stability. Based on the observed thermodynamic stabilities of the various conformational states, we showed that in the Q41N mutant, the N1 state is more significantly destabilized than the N2 state, resulting in an increase in the relative population of N2. Identifying the interactions controlling specific motions of a protein will facilitate molecular design to achieve functional dynamics beyond native state dynamics.

Direct high-pressure NMR observation of dipicolinic acid leaking from bacterial spore: A crucial step for thermal inactivation

A bacterial spore protects itself with an unusually high concentration (~10% in dry weight of spore) of dipicolinic acid (DPA), the release of which is considered the crucial step for inactivating it under mild pressure and temperature conditions. However, the process of how the spore releases DPA in response to pressure remains obscure. Here we apply 1H high-resolution high-pressure NMR spectroscopy, for the first time, to the spore suspension of Bacillus subtilis natto and monitor directly and in real-time the leaking process of DPA in response to pressure of 200MPa at 20°C. We find that about one third of the total DPA leaks immediately upon applying pressure, but that the rest leaks slowly in hrs upon decreasing the pressure. Once DPA is fully released from the spore, the proteins of the spore become easily denatured at a mild temperature, e.g., 80°C, much below the temperature commonly used to inactivate spores (121°C). The success of the present experiment opens a new avenue for studying bacterial spores and cells at the molecular level in response to pressure, temperature and other perturbations.