Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

Separation of small metabolites and lipids in spectra from biopsies by diffusion-weighted HR-MAS NMR: a feasibility study.

High Resolution Magic Angle Spinning (HR-MAS) NMR allows metabolic characterization of biopsies. HR-MAS spectra from tissues of most organs show strong lipid contributions that are overlapping metabolite regions, which hamper metabolite estimation. Metabolite quantification and analysis would benefit from a separation of lipids and small metabolites. Generally, a relaxation filter is used to reduce lipid contributions. However, the strong relaxation filter required to eliminate most of the lipids also reduces the signals for small metabolites. The aim of our study was therefore to investigate different diffusion editing techniques in order to employ diffusion differences for separating lipid and small metabolite contributions in the spectra from different organs for unbiased metabonomic analysis. Thus, 1D and 2D diffusion measurements were performed, and pure lipid spectra that were obtained at strong diffusion weighting (DW) were subtracted from those obtained at low DW, which include both small metabolites and lipids. This subtraction yielded almost lipid free small metabolite spectra from muscle tissue. Further improved separation was obtained by combining a 1D diffusion sequence with a T2-filter, with the subtraction method eliminating residual lipids from the spectra. Similar results obtained for biopsies of different organs suggest that this method is applicable in various tissue types. The elimination of lipids from HR-MAS spectra and the resulting less biased assessment of small metabolites have potential to remove ambiguities in the interpretation of metabonomic results. This is demonstrated in a reproducibility study on biopsies from human muscle.

Quantifying diffusion in biofilms : from model hydrogels to living biofilms

Les biofilms sont des communautés de microorganismes incorporés dans une matrice exo-polymérique complexe. Ils sont reconnus pour jouer un rôle important comme barrière de diffusion dans les systèmes environnementaux et la santé humaine, donnant lieu à une résistance accrue aux antibiotiques et aux désinfectants. Comme le transfert de masse dans un biofilm est principalement dû à la diffusion moléculaire, il est primordial de comprendre les principaux paramètres influençant les flux de diffusion. Dans ce travail, nous avons étudié un biofilm de Pseudomonas fluorescens et deux hydrogels modèles (agarose et alginate) pour lesquels l’autodiffusion (mouvement Brownien) et les coefficients de diffusion mutuels ont été quantifiés. La spectroscopie par corrélation de fluorescence a été utilisée pour mesurer les coefficients d'autodiffusion dans une volume confocal de ca. 1 m3 dans les gels ou les biofilms, tandis que les mesures de diffusion mutuelle ont été faites par cellule de diffusion. En outre, la voltamétrie sur microélectrode a été utilisée pour évaluer le potentiel de Donnan des gels afin de déterminer son impact sur la diffusion. Pour l'hydrogel d'agarose, les observations combinées d'une diminution du coefficient d’autodiffusion et de l’augmentation de la diffusion mutuelle pour une force ionique décroissante ont été attribuées au potentiel de Donnan du gel. Des mesures de l'effet Donnan (différence de -30 mV entre des forces ioniques de 10-4 et 10-1 M) et l'accumulation correspondante d’ions dans l'hydrogel (augmentation d’un facteur de 13 par rapport à la solution) ont indiqué que les interactions électrostatiques peuvent fortement influencer le flux de diffusion de cations, même dans un hydrogel faiblement chargé tel que l'agarose. Curieusement, pour un gel plus chargé comme l'alginate de calcium, la variation de la force ionique et du pH n'a donné lieu qu'à de légères variations de la diffusion de sondes chargées dans l'hydrogel. Ces résultats suggèrent qu’en influençant la diffusion du soluté, l'effet direct des cations sur la structure du gel (compression et/ou gonflement induits) était beaucoup plus efficace que l'effet Donnan. De même, pour un biofilm bactérien, les coefficients d'autodiffusion étaient pratiquement constants sur toute une gamme de force ionique (10-4-10-1 M), aussi bien pour des petits solutés chargés négativement ou positivement (le rapport du coefficient d’autodiffusion dans biofilm sur celui dans la solution, Db/Dw ≈ 85 %) que pour des nanoparticules (Db/Dw≈ 50 %), suggérant que l'effet d'obstruction des biofilms l’emporte sur l'effet de charge. Les résultats de cette étude ont montré que parmi les divers facteurs majeurs qui affectent la diffusion dans un biofilm environnemental oligotrophe (exclusion stérique, interactions électrostatiques et hydrophobes), les effets d'obstruction semblent être les plus importants lorsque l'on tente de comprendre la diffusion du soluté. Alors que les effets de charge ne semblaient pas être importants pour l'autodiffusion de substrats chargés dans l'hydrogel d'alginate ou dans le biofilm bactérien, ils ont joué un rôle clé dans la compréhension de la diffusion à travers l’agarose. L’ensemble de ces résultats devraient être très utiles pour l'évaluation de la biodisponibilité des contaminants traces et des nanoparticules dans l'environnement.

A MICROFLUIDIC METHOD TO MEASURE DIFFUSION IN HYDROGELS

A novel microfluidic method is proposed for studying diffusion of small molecules in a hydrogel. Microfluidic devices were prepared with semi-permeable microchannels defined by crosslinked poly(ethylene glycol) (PEG). Uptake of dye molecules from aqueous solutions flowing through the microchannels was observedoptically and diffusion of the dye into the hydrogel was quantified. To complement the diffusion measurements from the microfluidic studies, nuclear magnetic resonance(NMR) characterization of the diffusion of dye in the PEG hydrogels was performed. The diffusion of small molecules in a hydrogel is relevant to applications such asdrug delivery and modeling transport for tissue-engineering applications. The diffusion of small molecules in a hydrogel is dependent on the extent of crosslinking within the gel, gel structure, and interactions between the diffusive species and the hydrogel network. These effects were studied in a model environment (semi-infinite slab) at the hydrogelfluid boundary in a microfluidic device. The microfluidic devices containing PEG microchannels were fabricated using photolithography. The unsteady diffusion of small molecules (dyes) within the microfluidic device was monitored and recorded using a digital microscope. The information was analyzed with techniques drawn from digital microscopy and image analysis to obtain concentration profiles with time. Using a diffusion model to fit this concentration vs. position data, a diffusion coefficient was obtained. This diffusion coefficient was compared to those from complementary NMR analysis. A pulsed field gradient (PFG) method was used to investigate and quantify small molecule diffusion in gradient (PFG) method was used to investigate and quantify small molecule diffusion in hydrogels. There is good agreement between the diffusion coefficients obtained from the microfluidic methods and those found from the NMR studies. The microfluidic approachused in this research enables the study of diffusion at length scales that approach those of vasculature, facilitating models for studying drug elution from hydrogels in blood-contacting applications.

In-situ diffusion of HTO, 22Na+, Cs+ and I- in Opalinus Clay at the Mont Terri underground rock laboratory

The diffusion properties of the Opalinus Clay were studied in the underground research laboratory at Mont Terri (Canton Jura, Switzerland) and the results were compared with diffusion data measured in the laboratory on small-scale samples. The diffusion of HTO, Na-22(+), Cs+ and I- were investigated for a period of 10 months. The diffusion equipment used in the field experiment was designed in such a way that a solution of tracers was circulated through a sintered metal screen placed at the end of a borehole drilled in the formation. The concentration decrease caused by the diffusion of tracers into the rock could be followed with time and allowed first estimations of the effective diffusion coefficient. After 10 months, the diffusion zone was over-cored and the tracer profiles measured. From these profiles, effective diffusion coefficients and rock capacity factors Could be extracted by applying a two-dimensional transport model including diffusion and sorption. The simulations were done with the reactive transport code CRUNCH. In addition, results obtained from through-diffusion experiments oil small-sized samples with HTO, Cl-36(-) and Na-22(+) are presented and compared with the in situ data. In all cases. excellent agreement between the two data sets exists. Results for Cs+ indicated five times higher diffusion rates relative to HTO. Corresponding laboratory diffusion measurements are still lacking. However. our Cs+ data are in qualitative agreement wish through-diffusion data for Callovo-Oxfordian argillite rock samples. which also indicate significantly higher effective diffusivities for Cs+ relative to HTO.

Diffusion of HTO, Br-, I-, Cs+, Sr-85(2+) and Co-60(2+) in a clay formation: Results and modelling from an in situ experiment in Opalinus Clay

The migration of radioactive and chemical contaminants in clay materials and argillaceous host rocks is characterised by diffusion and retention processes. Valuable information on such processes can be gained by combining diffusion studies at laboratory scale with field migration tests. In this work, the outcome of a multi-tracer in situ migration test performed in the Opalinus Clay formation in the Mont Terri underground rock laboratory (Switzerland) is presented. Thus, 1.16 x 10(5) Bq/L of HTO, 3.96 x 10(3) Bq/L of Sr-85, 6.29 x 10(2) Bq/L of Co-60, 2.01 x 10(-3) mol/L Cs, 9.10 x 10(-4) mol/L I and 1.04 x 10(-3) mol/L Br were injected into the borehole. The decrease of the radioisotope concentrations in the borehole was monitored using in situ gamma-spectrometry. The other tracers were analyzed with state-of-the-art laboratory procedures after sampling of small water aliquots from the reservoir. The diffusion experiment was carried out over a period of one year after which the interval section was overcored and analyzed. Based on the experimental data from the tracer evolution in the borehole and the tracer profiles in the rock, the diffusion of tracers was modelled with the numerical code CRUNCH. The results obtained for HTO (H-3), I- and Br- confirm previous lab and in situ diffusion data. Anionic fluxes into the formation were smaller compared to HTO because of anion exclusion effects. The migration of the cations Sr-85(2+), Cs+ and Co-60(2+) was found to be governed by both diffusion and sorption processes. For Sr-85(2+), the slightly higher diffusivity relative to HTO and the low sorption value are consistent with laboratory diffusion measurements on small-scale samples. In the case of Cs+, the numerically deduced high diffusivity and the Freundlich-type sorption behaviour is also supported by ongoing laboratory data. For Co, no laboratory diffusion data were yet available for comparison; however, the modelled data suggests that Co-60(2+) sorption was weaker than would be expected from available batch sorption data. Overall, the results demonstrate the feasibility of the experimental setup for obtaining high-quality diffusion data for conservative and sorbing tracers. (C) 2007 Elsevier Ltd. All rights reserved.

Separation of small metabolites and lipids in spectra from biopsies by diffusion-weighted HR-MAS NMR: a feasibility study.

High Resolution Magic Angle Spinning (HR-MAS) NMR allows metabolic characterization of biopsies. HR-MAS spectra from tissues of most organs show strong lipid contributions that are overlapping metabolite regions, which hamper metabolite estimation. Metabolite quantification and analysis would benefit from a separation of lipids and small metabolites. Generally, a relaxation filter is used to reduce lipid contributions. However, the strong relaxation filter required to eliminate most of the lipids also reduces the signals for small metabolites. The aim of our study was therefore to investigate different diffusion editing techniques in order to employ diffusion differences for separating lipid and small metabolite contributions in the spectra from different organs for unbiased metabonomic analysis. Thus, 1D and 2D diffusion measurements were performed, and pure lipid spectra that were obtained at strong diffusion weighting (DW) were subtracted from those obtained at low DW, which include both small metabolites and lipids. This subtraction yielded almost lipid free small metabolite spectra from muscle tissue. Further improved separation was obtained by combining a 1D diffusion sequence with a T2-filter, with the subtraction method eliminating residual lipids from the spectra. Similar results obtained for biopsies of different organs suggest that this method is applicable in various tissue types. The elimination of lipids from HR-MAS spectra and the resulting less biased assessment of small metabolites have potential to remove ambiguities in the interpretation of metabonomic results. This is demonstrated in a reproducibility study on biopsies from human muscle.

NMR characterization of blends of poly(hydroxybutyrate-co-hydroxyvalerate) with poly(vinyl acetate)

The extent of mixing in blends of poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) (27% HV) and poly(vinyl acetate) (PVAc) has been measured using a number of different techniques, principally solid-state NMR. Differential scanning calorimetry DSC measurements indicated effective mixing of the polymer chains on a scale of several nanometres. The results of H-1 T-1 and H-1 T-1rho. measurements confirm intimate mixing of the chains. A change on blending in the H-1 T-1rho, and the H-1 NMR line width of the signal from the protons of PVAc was consistent with an increase in the amplitude and frequency of motion of this component. The PVAc chains reside within the inter-lamellar space, as confirmed by spin diffusion measurements after H-1 T-1rho preparation. (C) 2003 Society of Chemical Industry.

Aplicação da espectroscopia de ressonância magnética nuclear para estudos de difusão molecular em líquidos: a técnica DOSY

Diffusion coefficients provide uniquely detailed and easily interpreted information on molecular organization and phase structure. They are quite sensitive to structural changes, and to binding and association phenomena, in particular for liquid colloidal or macromolecular systems. This paper describes the principles of diffusion measurements in liquids by pulsed magnetic field gradient spin-echo (PFG-SE) NMR spectroscopy. The important PFG-SE technique known as DOSY is presented and discussed. This is a noninvasive technique that can provide individual multicomponent translational diffusion coefficients with good precision in a few minutes, without the need for radioactive isotopic labelling.

Photothermal Characterization of Nanogold Under Conditions of Resonant Excitation and Energy Transfer

We have performed thermal diffusion measurements of nanofluid containing gold and rhodamine 6G dye in various ratios. At certain concentrations, gold is nearly four times more efficient than water in dissipating small temperature fluctuations in a medium, and therefore it will find applications as heat transfer fluids. We have employed dual-beam mode-matched thermal lens technique for the present investigation. It is a sensitive technique in measuring photothermal parameters because of the use of a lowpower, stabilized laser source as the probe. We also present the results of fluorescence measurements of the dye in the nanogold environment.

Diffusionsgewichtete Helium-3 Magnetresonanztomographie zur Untersuchung der Lunge

Die diffusionsgewichtete Magnetresonanztomographie (MRT) mit dem hyperpolarisierten Edelgas-Isotop 3He ist ein neues Verfahren zur Untersuchung von Erkrankungen der Atem-wege und der Lunge. Die Diffusionsbewegung der 3He-Atome in den Luftwegen der Lunge wird durch deren Wände begrenzt, wobei diese Einschränkung sowohl von den Dimensionen der Atemwege als auch von den Messparametern abhängt. Man misst daher einen scheinbaren Diffusionskoeffizienten (Apparent Diffusion Coefficient, ADC) der kleiner ist als der Diffusionskoeffizient bei freier Diffusion. Der ADC gestattet somit eine qualitative Abschät-zung der Größe der Luftwege und deren krankhafte Veränderung, ohne eine direkte Abbil-dung der Luftwege selbst. Eine dreidimensionale Abbildung der räumlichen Verteilung von Lungenschädigungen wird dadurch möglich. Ziel der vorliegenden Arbeit war es, ein tieferes physikalisch fundiertes Verständnis der 3He-Diffusionsmessung zu ermöglichen und die Methode der diffusionsgewichteten 3He-MRT hin zur Erfassung des kompletten 3He-Diffusionstensors weiterzuentwickeln. Dazu wurde systematisch im Rahmen von Phantom- und tierexperimentellen Studien sowie Patientenmes-sungen untersucht, inwieweit unterschiedliche Einflussfaktoren das Ergebnis der ADC-Messung beeinflussen. So konnte beispielsweise nachgewiesen werden, dass residuale Luftströmungen am Ende der Einatmung keinen Einfluss auf den ADC-Wert haben. Durch Simulationsrechnungen konnte gezeigt werden, in welchem Maße sich die durch den Anregungspuls hervorgerufene Abnah-me der Polarisation des 3He-Gases auf den gemessenen ADC-Wert auswirkt. In einer Studie an lungengesunden Probanden und Patienten konnte die Wiederholbarkeit der ADC-Messung untersucht werden, aber auch der Einfluss von Gravitationseffekten. Diese Ergebnisse ermöglichen genauere Angaben über systematische und statistische Messfehler, sowie über Grenzwerte zwischen normalem und krankhaft verändertem Lungengewebe. Im Rahmen dieser Arbeit wurde die bestehende diffusionsgewichtete Bildgebung methodisch zur Erfassung des kompletten Diffusionstensors von 3He in der Lunge weiterentwickelt. Dies war wichtig, da entlang der Luftwege weitestgehend freie Diffusion vorherrscht, während senkrecht zu den Luftwegen die Diffusion eingeschränkt ist. Mit Hilfe von Simulationsrech-nungen wurde der kritische Einfluss von Rauschen in den MRT-Bildern auf die Qualität der Messergebnisse untersucht. Diese neue Methodik wurde zunächst an einem Phantom beste-hend aus einem Bündel aus Glaskapillaren, deren innerer Durchmesser mit dem des mensch-lichen Azinus übereinstimmt, validiert. Es ergab sich eine gute Übereinstimmung zwischen theoretischen Berechnungen und experimentellen Ergebnissen. In ersten Messungen am Menschen konnten so unterschiedliche Anisotropiewerte zwischen lungengesunden Proban-den und Patienten gefunden werden. Es zeigte sich eine Tendenz zu isotroper Diffusion bei Patienten mit einem Lungenemphysem. Zusammenfassend tragen die Ergebnisse der vorliegenden Arbeit zu einem besseren Ver-ständnis der ADC-Messmethode bei und helfen zukünftige Studien aufgrund des tieferen Verständnisses der die 3He Messung beeinflussenden Faktoren besser zu planen.

Amyloid fibril formation by an SH3 domain

The SH3 domain is a well characterized small protein module with a simple fold found in many proteins. At acid pH, the SH3 domain (PI3-SH3) of the p85α subunit of bovine phosphatidylinositol 3-kinase slowly forms a gel that consists of typical amyloid fibrils as assessed by electron microscopy, a Congo red binding assay, and x-ray fiber diffraction. The soluble form of PI3-SH3 at acid pH (the A state by a variety of techniques) from which fibrils are generated has been characterized. Circular dichroism in the far- and near-UV regions and 1H NMR indicate that the A state is substantially unfolded relative to the native protein at neutral pH. NMR diffusion measurements indicate, however, that the effective hydrodynamic radius of the A state is only 23% higher than that of the native protein and is 20% lower than that of the protein denatured in 3.5 M guanidinium chloride. In addition, the A state binds the hydrophobic dye 1-anilinonaphthalene-8-sulfonic acid, which suggests that SH3 in this state has a partially formed hydrophobic core. These results indicate that the A state is partially folded and support the hypothesis that partially folded states formed in solution are precursors of amyloid deposition. Moreover, that this domain aggregates into amyloid fibrils suggests that the potential for amyloid deposition may be a common property of proteins, and not only of a few proteins associated with disease.

Chloride resistance and durability of cement paste and concrete containing metakaolin

Metakaolin (MK), a calcined clay, was included as a partial cement replacement material, at up to 20% by weight of binder, in cement pastes and concrete, and its influence on the resistance to chloride ingress investigated. Reductions in effective chloride diffusion coefficients through hardened cement paste were obtained for binary blends and by combining OPC, MK and a second cement replacement material of pulverised fuel ash or ground granulated blast furnace slag. Steady state oxygen diffusion measurements through hardened cement pastes measured using an electrochemical cell showed that the interaction between charged species and the pore surfaces is a major factor in determining chloride diffusion rate. Rheology of the binder, particularly at high MK replacement levels, was found to have a dramatic influence on the diffusion performance of cement pastes. It was concluded that plasticising admixtures are essential for adequate dispersion of MK in cement pastes. Chloride concentration profile analysis of the concrete cylinders, exposed to sodium chloride solution for one year, was employed to obtain apparent chloride diffusion coefficients for concrete specimens. MK was found to reduce the depth of chloride penetration into concrete when compared with that of unblended mixes. Corrosion rate and corrosion potential measurements were taken on steel bars embedded in concrete exposed to a saline environment under conditions of cyclic wetting and drying. The initiation time for corrosion was found to be significantly longer for MK blended mixes than for plain OPC systems. The aggregate-paste interfacial zone of MK blended systems was investigated by steady state diffusion of chloride ions through mortar containing glass beads as model aggregate. For the model aggregate specimens tested the work confirmed the hypothesis that properties of the bulk paste are the controlling factors in ionic diffusion through mortar.