A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

NMR relaxation time measurements of solvent effects in an organocatalysed asymmetric aldol reaction over silica SBA-15 supported proline

Immobilisation of organocatalysts onto solid supports represents a very promising solution to tackle their low productivity by enabling their reuse. Herein, the use of NMR relaxation measurements, coupled with reaction...

New Insight into Li+ Dynamics in Lithium Bimetal Phosphate

Substitution of iron by other transition metals within the remarkably stable olivine framework is of interest considering the expected gain in energy density. However, manganese rich olivine materials suffer from sluggish redox kinetics, leading to electrochemical performances at high current densities which are below expectations. The source of the kinetic limitations is not clear, with multiple processes having been proposed, including low bulk electronic conductivity, structural instability of Mn3+ and a phase transition mechanism. This study employed 7Li MAS NMR relaxation techniques to indirectly probe Li+ dynamics using various stoichiometry of chemically prepared LixMnyFe1-yPO4 (0 ≤ (x, y) ≤ 1). Focusing on the particle level, the aim was to understand how the different crystal phases, alongside the Mn structural contribution, influence Li+ transport at each stage of the oxidation process. Significantly, the formation of an olivine solid solution with vacancies within this progression gave rise to a faster 7Li transverse relaxation derived from superior Li+ motion.

Evaluate Wettability and Production Potential of Tight Reservoirs Through Spontaneous Imbibition Using Time-Lapse NMR and Other Measurements

Several studies have shown that rock-fluid interactions in tight rocks are influenced by the natural wettability behavior of the various pore systems. Studying the water/oil displacement on a smaller scale using core plug imbibition and monitoring with NMR is very insightful in evaluating wettability and distinguishing pore modes and rock types based on their fluid affinity. Extending learnings from plug-scale imbibition process to reservoir production behavior requires understanding of the underlying compositional and/or textural parameters controlling the wettability. This paper presents a systematic study of spontaneous imbibition of oil and water in core plugs procured from several tight and organic-rich reservoirs with varying mineral composition and organic content. The experiment comprised three identical core plugs from the same depth undergoing multiple fluid imbibition cycles with one plug starting in produced brine, the second one in produced crude and the last one in decane. Sample weights were continuously monitored and when stable, a sample which was in brine was moved to crude and the one in crude was moved to brine. This process was repeated for four cycles so that samples that started in brine finally ended up in crude and those that started in crude ended up in brine. The saturation changes and rock-fluid interaction in different fluid types were monitored using a 12 MHz NMR spectrometer. The 12 MHz NMR allowed very accurate partitioning of the oil-filled and water-filled porosity in these tight rocks, which was essential for the wettability analysis. The rate and extent of saturation changes varied significantly from sample to sample. The comparison between the companion plugs imbibing either higher amounts of oil or water revealed the fluid affinity of each sample. We computed the ratio of the net incremental fluid fraction to the total porosity to represent the dominant pore wetting system for rock samples at a given depth. We measured organic content and mineralogy of the samples and analyzed the matrix effect on wettability. We analyzed the post-imbibition NMR relaxation times (T1,T2) of individual fluid types and integrated with matrix properties to evaluate oil and water mobilities. We found predicted fluid mobilities to be consistent with the observed production from wells drilled in the different reservoirs and rock types. We observed most samples attain 100% fluid saturation within two to four cycles and almost all the samples at a given depth took up very similar water volumes irrespective of whether the companion plugs started in brine or crude. The process highlighted that water-wet pores governed the final water saturation, which was strongly correlated with total clay. The amount of organic content and carbonate minerals influenced the oil uptake and its relative mobility. For samples that started in decane, decane was imbibed faster and caused samples to attain higher oil saturation than samples that started in crude.

Temperature Dependence of Nuclear Magnetic Resonance Relaxation Time in Carbonate Reservoirs

Summary Nuclear magnetic resonance (NMR)-based interpretation models are commonly calibrated using laboratory ambient core NMR measurements. For applying the core calibrated models to downhole NMR logging interpretation, the difference between the NMR responses measured at ambient and reservoir temperature needs to be evaluated. The temperature dependence of NMR relaxation time in high-quality (HQ) carbonate reservoirs has been studied, and NMR temperature dependence models were established using data analytic methods. In this paper, we extend our early studies on temperature dependence of NMR relaxation time to low-quality (LQ) carbonate formations. For more than 95% of the LQ samples investigated, NMR relaxation time shows a positive correlation with temperature. The correlation is similar to that observed in HQ carbonate rocks but slightly less significant. Temperature-dependent correlations for predicting the geometric mean of NMR transverse relaxation time (T2,GM) from a measured temperature to any other temperature were derived from HQ to LQ carbonate rocks independently first, then a unified T2,GM correlation was derived including both the HQ and LQ carbonate reservoirs. Predicting NMR transverse relaxation time T2 distribution from one temperature to other temperatures was achieved using a dimension reduction approach involving the principal component analysis (PCA) technique. It was found that the T2 distributions at any given temperature for both HQ and LQ carbonate reservoirs can be predicted robustly from the T2 distributions at the ambient temperature by representing the T2 distributions with principal components (PCs) at the ambient temperature and then using these PCs to predict the PCs at a different temperature. The optimal number of PC components depends on the multimodality of the T2distribution. This work extends the validity range of the data analytic methods, in particular parameter and dimension reduction methods, that quantify the temperature dependence of carbonate NMR properties. The new NMR temperature model enables the integration of NMR laboratory studies and downhole measurements for advanced petrophysical analyses in a wide range of carbonate reservoirs.

How much entropy is contained in NMR relaxation parameters?

Solution-state NMR relaxation experiments are the cornerstone to study internalprotein dynamics at atomic resolution on time scales that are faster than the overallrotational tumbling time,τR. Since the motions described by NMR relaxation pa-rameters are connected to thermodynamic quantities like conformational entropies, thequestion arises how much of the total entropy is contained within this tumbling time.Using all-atom molecular dynamics (MD) simulations of T4 lysozyme, we found thatentropy build-up is rather fast for the backbone, such that the majority of the entropyis indeed contained in the short-time dynamics. In contrast, the contribution of slowdynamics of side chains on time scales beyondτRon the side chain conformationalentropy is significant and should be taken into account for the extraction of accuratethermodynamic properties.

Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

The conformational heterogeneity of a folded protein can affect both its function but also stability and folding. We recently discovered and characterized a stabilized double mutant (L49I/I57V) of the protein CI2 and showed that state-of-the-art prediction methods could not predict the increased stability relative to the wild-type protein. Here we have examined whether changed native state dynamics, and resulting entropy changes, can explain the stability changes in the double mutant protein, as well as the two single mutant forms. We have combined NMR relaxation measurements of the ps-ns dynamics of amide groups in the backbone and the methyl groups in the side-chains with molecular dynamics simulations to quantify the native state dynamics. The NMR experiments reveal that the mutations have different effects on the conformational flexibility of CI2: A reduction in conformational dynamics (and entropy) of the native state of L49I variant correlates with its decreased stability, while increased dynamics of the I57V and L49I/I57V variants correlates with their increased stability. These findings suggest that explicitly accounting for changes in native state entropy might be needed to improve the predictions of the effect of mutations on protein stability.