Chemical Exchange Rates Research Articles

The hydrogen-bonding dynamics of water to a nitrile-functionalized electrode is modulated by voltage according to ultrafast 2D IR spectroscopy.

We report the hydrogen-bonding dynamics of water to a nitrile-functionalized and plasmonic electrode surface as a function of applied voltage. The surface-enhanced two-dimensional infrared spectra exhibit hydrogen-bonded and non-hydrogen-bonded nitrile features in similar proportions, plus cross peaks between the two. Isotopic dilution experiments show that the cross peaks arise predominantly from chemical exchange between hydrogen-bonded and non-hydrogen-bonded nitriles. The chemical exchange rate depends upon voltage, with the hydrogen bond of the water to the nitriles breaking 2 to 3 times slower (>63 vs. 25 ps) under a positive as compared to a negative potential. Spectral diffusion created by hydrogen-bond fluctuations occurs on a ~1 ps timescale and is moderately potential-dependent. Timescales from molecular dynamics simulations agree qualitatively with the experiment and show that a negative voltage causes a small net displacement of water away from the surface. These results show that the voltage applied to an electrode can alter the timescales of solvent motion at its interface, which has implications for electrochemically driven reactions.

Measuring chemical exchange saturation transfer exchange rates in the human brain using a particle swarm optimisation algorithm.

The z-spectrum contains many pools with different exchange rates and T2 values, which can make it difficult to interpret in vivo data and complicates the design of experiments aimed at providing sensitivity to one pool. This work aims to characterise the main pools observable with MRI at 7T in the human brain. To achieve this, we acquired z-spectra at multiple saturation powers in the human brain at 7T. We used simulations to optimise the use of particle swarm optimisation (PSO) to fit these data, validating this approach using further simulations and creatine phantoms. We then used the PSO to fit data from grey and white matter for the pool size, exchange rate, and T2 of five proton pools (magnetisation transfer, amides, amines, nuclear Overhauser enhancement NOE-3.5ppm and NOE-1.7ppm in addition to water). We then devised an approach for using PSO to fit z-spectra while limiting the computational burden, and we investigated the sensitivity of the fit to T2 and k for three overlapping pools. We used this to measure the exchange rate of creatine and to show that it varied with temperature, as expected. In the brain we measured a significantly larger pool size in white matter than in grey matter for the magnetisation transfer pool and the NOE-3.5ppm pool. For all other parameters we found no significant difference between grey and white matter. We showed that PSO can be used to fit z-spectra acquired at a range of B1 to provide information about peak position, amplitude, exchange rate, and T2 in vivo in the human brain. These data could provide more sensitivity to change in some clinical conditions and will also provide key information for further experimental design.

Investigation of the influence of pH on the properties and morphology of gelatin hydrogels

AbstractThe behavior of gelatin hydrogels is influenced by the charges located on the amino acid side chains throughout the gelatin molecules. The presence and distribution of ionisable side chains influences the surface activity of gelatin and ultimately determines the material properties. Herein, we report the influence of pH on mechanical properties as studied by texture analysis supported by data from polarimetry, zeta potential, pH titrations and NMR experiments. When adjusted to more extreme pH values (pH 2 and 12), softer gelatin blocks were observed. However, at pH values close to the isoelectric point (pH 5–10), the material is firmer. This behavior is related to the helical content. At pH 2 and pH 12 the surface of the gelatin carries a net charge, positive and negative, respectively, that inhibits the formation of tight helices and lowers the physical crosslink network density. Chemical shift perturbations were observed for the acidic amino acids glutamic and aspartic acid, under acidic pH, where their peaks shifted to higher ppm. Intense amide signals were observed at acidic pH but diminished with increasing pH. This was due to an increase in the rate of chemical exchange between the solvent and peptide amide protons as the pH increases.

Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy

Base pairs are fundamental building blocks of RNA. The base pairs of low stability are often critical in RNA functions. Here, we develop a solid-state NMR-based water-RNA exchange spectroscopy (WaterREXSY) to characterize RNA in solid. The approach uses different chemical exchange rates between iminos and waterto evaluate base pair stability; the less stable ones would exchange more frequently, leading to stronger cross-peaks on WaterREXSY. Applied to the riboA71-adenine complex (the 71nt-aptamer domain of add adenine riboswitch from Vibrio vulnificus), the U47⋅U51 base pair, which is critical in ligand binding, was found to be less stable than other base pairs. The imino-water exchange rates of U47 at different temperatures are about 500-800 s-1, indeed indicative of low stability. This implies a highly complex and plastic triad involving U47⋅U51 and that the opening of the U47⋅U51 base pair may be the early stage of ligand release.

Detection of tissue pH with quantitative chemical exchange saturation transfer magnetic resonance imaging.

Chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) has emerged as a novel means for sensitive detection of dilute labile protons and chemical exchange rates. By sensitizing to pH-dependent chemical exchange, CEST MRI has shown promising results in monitoring tissue statuses such as pH changes in disorders like acute stroke, tumor, and acute kidney injury. This article briefly reviews the basic principles for CEST imaging and quantitative measures, from the simplistic asymmetry analysis to multipool Lorentzian decoupling and quasi-steady-state reconstruction. In particular, the advantages and limitations of commonly used quantitative approaches for CEST applications are discussed.

Zero-Field NMR of Urea: Spin-Topology Engineering by Chemical Exchange.

Well-resolved and information-rich J-spectra are the foundation for chemical detection in zero-field NMR. However, even for relatively small molecules, spectra exhibit complexity, hindering the analysis. To address this problem, we investigate an example biomolecule with a complex J-coupling network—urea, a key metabolite in protein catabolism—and demonstrate ways of simplifying its zero-field spectra by modifying spin topology. This goal is achieved by controlling pH-dependent chemical exchange rates of 1H nuclei and varying the composition of the D2O/H2O mixture used as a solvent. Specifically, we demonstrate that by increasing the proton exchange rate in the [13C,15N2]-urea solution, the spin system simplifies, manifesting through a single narrow spectral peak. Additionally, we show that the spectra of 1H/D isotopologues of [15N2]-urea can be understood easily by analyzing isolated spin subsystems. This study paves the way for zero-field NMR detection of complex biomolecules, particularly in biofluids with a high concentration of water.

The use of variable delay multipulse chemical exchange saturation transfer for separately assessing different CEST pools in the human brain at 7T.

PurposeCurrent challenges of in vivo CEST imaging include overlapping signals from different pools. The overlap arises from closely resonating pools and/or the broad magnetization transfer contrast (MTC) from macromolecules. This study aimed to evaluate the feasibility of variable delay multipulse (VDMP) CEST to separately assess solute pools with different chemical exchange rates in the human brain in vivo, while mitigating the MTC.MethodsVDMP saturation buildup curves were simulated for amines, amides, and relayed nuclear Overhauser effect. VDMP data were acquired from glutamate and bovine serum albumin phantoms, and from six healthy volunteers at 7T. For the in vivo data, MTC removal was performed via a three‐pool Lorentzian fitting. Different B1 amplitudes and mixing times were used to evaluate CEST pools with different exchange rates.ResultsThe results show the importance of removing MTC when applying VDMP in vivo and the influence of B1 for distinguishing different pools. Finally, the optimal B1 and mixing times to effectively saturate slow‐ and fast‐exchanging components are also reported. Slow‐exchanging amides and rNOE components could be distinguished when using B1 = 1 μT and tmix = 10 ms and 40 ms, respectively. Fast‐exchanging components reached the highest saturation when using a B1 = 2.8 μT and tmix = 0 ms.ConclusionVDMP is a powerful CEST‐editing tool, exploiting chemical exchange‐rate differences. After MTC removal, it allows separate assessment of slow‐ and fast‐exchanging solute pools in in vivo human brain.

Low duty cycle pulse trains for exchange rate insensitive chemical exchange saturation transfer MRI.

To introduce and validate a pulse scheme that uses low duty cycle trains of π-pulses to achieve saturation that is relatively insensitive to exchange rate yet linearly dependent on labile proton concentration. Simulations were performed to explore the exchange rate sensitivity of π-pulse trains and continuous wave chemical exchange saturation transfer (CEST) signals. Creatine phantoms with varying pH and varying concentrations were imaged to demonstrate pH insensitivity and concentration dependence of low duty cycle π-pulse saturation. Simulations show decreasing the duty cycle of π-pulse saturation decreases peak sensitivity to exchange rate, and this range of insensitivity can be tuned to different exchange rates through average B1 power. The range of insensitivity is unaffected by changes in relaxation and magnetization transfer, while the sensitivity of CEST signal maintains linear dependence on labile proton concentration. Under B1,avg = 0.48 μT, 30mM creatine with pHs ranging between 6.36 and 8.21 exhibited CEST contrast ranging between ~6 and 11% under continuous wave and ~4% across all pHs using 10% duty cycle π-pulses. Imaging these phantoms using duty cycles of 5, 10, 25, and 50% showed decreasing pH sensitivity with decreased duty cycle. Creatine phantoms with varied concentrations and pHs reveal that π-pulse train saturation exhibited stricter correlation to concentration at lower DCs. Low DC π-pulse train is an easy-to-implement way of providing labile proton concentration-dependent CEST MRI signal that is insensitive to exchange rate. This approach can be useful in studies where a change of chemical exchange rate may interfere with accurate assessments of physiology or pathology.

Intermolecular dynamics and paramagnetic properties of Tm-Na heterometallic complex with macrocyclic ligand by 23Na dynamic NMR

The temperature dependence of lanthanide-induced shifts (LIS) and chemical exchange rate constants are studied. The analysis of chemical exchange rate constants was carried out using the method of analysis of the bandshape taking into account the temperature change in the LIS. The value of Gibbs free energy for the activation of intermolecular dynamics is ΔG≠(298 K) = 55 ± 2 kJ/mol. Method of analysis of the bandshape taking into account the temperature change in the paramagnetic lanthanide-induced shifts used for estimation the activation energy of intermolecular dynamics ΔG≠(298 K) = 55 ± 2 kJ/mol.

Determining chemical exchange rate constants in nanoemulsions using nuclear magnetic resonance.

In this work, the second-order kinetics of molecules exchanging between chemically distinct microenvironments, such as those found in nanoemulsions, is studied using nuclear magnetic resonance (NMR). A unique aspect of NMR exchange studies in nanoemulsions is that the difference in molecular resonance frequencies between the two phases, which determines whether the exchange is fast, intermediate, or slow on the NMR timescale, can depend upon the emulsion droplet composition, which is also determined by the kinetic exchange constants themselves. Within the fast-exchange regime, changes in resonance frequencies and line widths with dilution were used to extract the exchange rate constants from the NMR spectra in a manner analogous to determining the kinetic parameters in NMR ligand binding experiments. As a demonstration, the kinetic exchange parameters of isoflurane release from an emulsification of isoflurane and perflurotributylamine (FC43) were determined using NMR dilution and diffusion studies.

Concentration-Dependent Structural Transition of the HIV-1 gp41 MPER Peptide into α-Helical Trimers.

The membrane proximal external region (MPER) of HIV-1 gp41 contains epitopes for at least four broadly neutralizing antibodies. Depending on solution conditions and construct design, different structures have been reported for this segment. We show that in aqueous solution the MPER fragment (gp160660-674 ) exists in a monomer-trimer equilibrium with an association constant in the micromolar range. Thermodynamic analysis reveals that the association is exothermic, more favorable in D2 O than H2 O, and increases with ionic strength, indicating hydrophobically driven intermolecular interactions. Circular dichroism, 13 Cα chemical shifts, NOE, and hydrogen exchange rates reveal that MPER undergoes a structural transition from predominately unfolded monomer at low concentrations to an α-helical trimer at high concentrations. This result has implications for antibody recognition of MPER prior to and during the process where gp41 switches from a pre-hairpin intermediate to its post-fusion 6-helical bundle state.

Concentration‐Dependent Structural Transition of the HIV‐1 gp41 MPER Peptide into α‐Helical Trimers

AbstractThe membrane proximal external region (MPER) of HIV‐1 gp41 contains epitopes for at least four broadly neutralizing antibodies. Depending on solution conditions and construct design, different structures have been reported for this segment. We show that in aqueous solution the MPER fragment (gp160660–674) exists in a monomer‐trimer equilibrium with an association constant in the micromolar range. Thermodynamic analysis reveals that the association is exothermic, more favorable in D2O than H2O, and increases with ionic strength, indicating hydrophobically driven intermolecular interactions. Circular dichroism, 13Cα chemical shifts, NOE, and hydrogen exchange rates reveal that MPER undergoes a structural transition from predominately unfolded monomer at low concentrations to an α‐helical trimer at high concentrations. This result has implications for antibody recognition of MPER prior to and during the process where gp41 switches from a pre‐hairpin intermediate to its post‐fusion 6‐helical bundle state.

Quantification of creatine kinase reaction rate in mouse hindlimb using phosphorus-31 magnetic resonance spectroscopic fingerprinting.

The goal of this study was to evaluate the accuracy, reproducibility, and efficiency of a 31 P magnetic resonance spectroscopic fingerprinting (31 P-MRSF) method for fast quantification of the forward rate constant of creatine kinase (CK) in mouse hindlimb. The 31 P-MRSF method acquired spectroscopic fingerprints using interleaved acquisition of phosphocreatine (PCr) and γATP with ramped flip angles and a saturation scheme sensitive to chemical exchange between PCr and γATP. Parameter estimation was performed by matching the acquired fingerprints to a dictionary of simulated fingerprints generated from the Bloch-McConnell model. The accuracy of 31 P-MRSF measurements was compared with the magnetization transfer (MT-MRS) method in mouse hindlimb at 9.4 T (n = 8). The reproducibility of 31 P-MRSF was also assessed by repeated measurements. Estimation of the CK rate constant using 31 P-MRSF (0.39 ± 0.03 s-1 ) showed a strong agreement with that using MT-MRS measurements (0.40 ± 0.05 s-1 ). Variations less than 10% were achieved with 2 min acquisition of 31 P-MRSF data. Application of the 31 P-MRSF method to mice subjected to an electrical stimulation protocol detected an increase in CK rate constant in response to stimulation-induced muscle contraction. These results demonstrated the potential of the 31 P-MRSF framework for rapid, accurate, and reproducible quantification of the chemical exchange rate of CK in vivo.

N-Aryl Amides as Chemical Exchange Saturation Transfer Magnetic Resonance Imaging Contrast Agents.

Chemical exchange saturation transfer (CEST) MRI has recently emerged as a versatile molecular imaging approach in which diamagnetic compounds can be utilized to generate an MRI signal. To expand the scope of CEST MRI applications, herein, we systematically investigated the CEST properties of N-aryl amides with different N-aromatic substitution, revealing their chemical shifts (4.6-5.8 ppm) and exchange rates (up to thousands s-1 ) are favorable to be used as CEST agents as compared to alkyl amides. As the first proof-of-concept study, we used CEST MRI to detect the enzymatic metabolism of the drug acebutolol directly by its intrinsic CEST signal without any chemical labeling. Our study implies that N-aryl amides may enable the label-free CEST MRI detection of the metabolism of many N-aryl amide-containing drugs and a variety of enzymes that act on N-aryl amides, greatly expanding the scope of CEST MR molecular imaging.

Pulse sequences for measuring exchange rates between proton species: From unlocalised NMR spectroscopy to chemical exchange saturation transfer imaging

Within the field of NMR spectroscopy, the study of chemical exchange processes through saturation transfer techniques has a long history. In the context of MRI, chemical exchange techniques have been adapted to increase the sensitivity of imaging to small fractions of exchangeable protons, including the labile protons of amines, amides and hydroxyls. The MR contrast is generated by frequency-selective irradiation of the labile protons, which results in a reduction of the water signal associated with transfer of the labile protons’ saturated magnetization to the protons of the surrounding free water. The signal intensity depends on the rate of chemical exchange and the concentration of labile protons as well as on the properties of the irradiation field. This methodology is referred to as CEST (chemical exchange saturation transfer) imaging. Applications of CEST include imaging of molecules with short transverse relaxation times and mapping of physiological parameters such as pH, temperature, buffer concentration and chemical composition due to the dependency of this chemical exchange effect on all these parameters. This article aims to describe these effects both theoretically and experimentally. In depth analysis and mathematical modelling are provided for all pulse sequences designed to date to measure the chemical exchange rate. Importantly, it has become clear that the background signal from semi-solid protons and the presence of the Nuclear Overhauser Effect (NOE), either through direct dipole-dipole mechanisms or through exchange-relayed signals, complicates the analysis of CEST effects. Therefore, advanced methods to suppress these confounding factors have been developed, and these are also reviewed. Finally, the experimental work conducted both in vitro and in vivo is discussed and the progress of CEST imaging towards clinical practice is presented.

Chemical exchange induced Hahn echo modulation in pulsed electron paramagnetic resonance experiment

Triarylmethyl (TAM) radicals are probes well suited to study microenvironment parameters using pulse electron paramagnetic resonance (EPR) due to their long relaxation times. Here, we are reporting the study of relaxation properties of monophosphonated TAM radicals in the presence of chemical exchange processes. The dependence of Hahn and inversion recovery echo on the solution pH and the chemical exchange rate are discussed. The modulation of Hahn echo intensity in solutions due to chemical exchange is observed in pulse EPR experiments. An analysis of the Hahn echo intensity decay allows for the quantitative determination of the chemical exchange rate and solution pH value.

Validation of Enthalpy-Entropy Compensation Mechanism in Partial Amide Bond Rotation.

The concept of enthalpy–entropy compensation (EEC) is one of the highly debated areas of thermodynamics. The conformational change due to restricted double-bond rotation shows a classic two-site chemical exchange phenomenon and has been extensively studied. Fifty-four analogs of N,N-diethyl-m-toluamide (DEET) as a model system were synthesized to study the thermodynamics of the partial amide bond character using nuclear magnetic resonance (NMR) spectroscopy. Line-shape analysis as a function of temperature is used to estimate the chemical exchange. Eyring analysis was then used to convert the chemical exchange rates to determine the transition state enthalpy and entropy of the molecules. The experimental design follows selective variations that perturb one aspect of the molecular system and its influence on the observed thermodynamic effect. The results of the study demonstrate that amide bond resonance in analogs of DEET follows an EEC mechanism. Simple modifications made to DEET’s structural motif alter both the enthalpy and entropy of the system and were limited overall to a temperature compensation factor, Tβ = 292.20 K, 95% CI [290.66, 293.73]. We suggest EEC as a model to describe the kinetic compensation seen in chemical exchange phenomena in analogs of DEET.

Sensitivity-enhanced three-dimensional and carbon-detected two-dimensional NMR of proteins using hyperpolarized water

Signal enhancements of up to two orders of magnitude in protein NMR can be achieved by employing HDO as a vector to introduce hyperpolarization into folded or intrinsically disordered proteins. In this approach, hyperpolarized HDO produced by dissolution-dynamic nuclear polarization (D-DNP) is mixed with a protein solution waiting in a high-field NMR spectrometer, whereupon amide proton exchange and nuclear Overhauser effects (NOE) transfer hyperpolarization to the protein and enable acquisition of a signal-enhanced high-resolution spectrum. To date, the use of this strategy has been limited to 1D and 1H-15N 2D correlation experiments. Here we introduce 2D 13C-detected D-DNP, to reduce exchange-induced broadening and other relaxation penalties that can adversely affect proton-detected D-DNP experiments. We also introduce hyperpolarized 3D spectroscopy, opening the possibility of D-DNP studies of larger proteins and IDPs, where assignment and residue-specific investigation may be impeded by spectral crowding. The signal enhancements obtained depend in particular on the rates of chemical and magnetic exchange of the observed residues, thus resulting in non-uniform ‘hyperpolarization-selective’ signal enhancements. The resulting spectral sparsity, however, makes it possible to resolve and monitor individual amino acids in IDPs of over 200 residues at acquisition times of just over a minute. We apply the proposed experiments to two model systems: the compactly folded protein ubiquitin, and the intrinsically disordered protein (IDP) osteopontin (OPN).

Modeling the Dependency Structure between Stocks of Chemical Products Return, Oil Price and Exchange Rate Growth in Iran; an Application of Vine Copula

Modeling the Dependency Structure between Stocks of Chemical Products Return, Oil Price and Exchange Rate Growth in Iran; an Application of Vine Copula

Harnessing chemical exchange: 19F magnetic resonance OFF/ON zinc sensing with a Tm(iii) complex.

A fluorinated, thulium(iii) complex (Tm-PFZ-1) serves as an off-on 19F magnetic resonance probe for Zn(ii). Rapid exchange among different conformations combined with paramagnetic relaxation and chemical shift effects of Tm(iii) effectively eliminate the 19F NMR/MRI signal in Tm-PFZ-1. Chelation of Zn(ii) induces increased structural rigidity and reduces exchange rate, affording a robust 19F NMR/MRI signal. Tm-PFZ-1 represents a first-in-class paramagnetic 19F MR agent that exploits a novel sensing mechanism for Zn(ii) and is the first 19F MR-based scaffold to provide an "off-on" response to Zn(ii) in aqueous solution.