The biological functions of proteins often rely on structural changes and the rates at which these conformational changes occur. Studies show that regions of a protein which are known to be involved in enzyme catalysis or in contact with the substrate are identifiable by NMR spectroscopy to be more flexible, evidenced through measuring order parameters of specific bond vectors. While generalized NMR can allow for detailed characterization of the extent and time scales of these conformational fluctuations, NMR cannot easily produce the structures of sparsely populated intermediates nor can it produce explicit complex atomistic-level mechanisms needed for the full understanding of such processes. Practically, preparing a protein with appropriate isotropic enrichment to study a set of specific bond vectors experimentally is challenging as well. Oftentimes, measuring the dynamics of neighboring bond vectors are necessitated. Detailed studies of the coupling interactions among specific residues and protein regions can be fulfilled by the use of molecular dynamics (MD) simulations. However, MD simulations rely on the ergodic hypothesis to mimic experimental conditions, requiring long simulation times. Simulations are additionally limited by the availability of accurate and reliable molecular mechanics force fields, which continue to be improved to better match experimental data. Much can also be learned from chemical theory and simulations to improve the methods in which experimental data is processed and analyzed. The overarching goals of this thesis are to improve upon the results generated by existing methods in NMR spin relaxation spectroscopy, whether that be through: (i) improving analytical techniques of raw NMR data or through (ii) supporting experimental results with atomistically-detailed MD simulations. The majority of this work is exemplified through the protein Escherichia coli ribonuclease HI (ecRNH). Ribonuclease HI (RNase H) is a conserved endonuclease responsible for cleaving the RNA strand of DNA/RNA hybrids in many biological processes, including reverse transcription of the viral genome in retroviral reverse transcriptases and Okazaki fragment processing during DNA replication of the lagging strand. RNase H belongs to a broader superfamily of nucleotidyl-transferases with conserved structure and mechanism, including retroviral integrases, Holliday junction resolvases, and transposases. RNase H has historically been the subject of many investigations in folding, structure, and dynamics. In support of the first aim, we discuss new methods of obtaining more precise experimental results for order parameters and time constants for the ILV methyl groups. Deuterium relaxation rate constants are determined by the spectral density function for reorientation of the C-D bond vector at zero, single-quantum, and double-quantum 2H frequencies. We interpolate relaxation rates measured at available NMR spectrometer frequencies in order to perform a joint single/double-quantum analysis. This yields approximately 10-15% more precise estimates of model-free parameters and consequently provides a general strategy for further interpolation and extrapolation of data gathered from existing NMR spectrometers for analysis of 2H spin relaxation data in biological macromolecules. In support of the second aim, we calculate autocorrelation functions and generalized order parameters for the ILV methyl side chain groups from MD simulation trajectories to assess the orientational motions of the side chain bond vectors. We demonstrate that motions of the side chain bond vectors can be separated into: (i) fluctuations within a given dihedral angle rotamer, (ii) jumps among the different rotamers, and (iii) motions from the protein backbone itself, through the C-alpha carbon. We are able to match order parameters of constitutive motions to conventionally calculated order parameters with an R2= 0.9962, 0.9708, and 0.9905 for Valine, Leucine, and Isoleucine residues, respectively. Some longer side chain residues such as Leucine and Isoleucine have correlated χ1 and χ2 dihedral angle rotational motions. This provides a method of evaluating the relative contributions of each constitutive motion towards the overall flexibility of a side chain. Multiple contributors of motion are possible for intermediate and low order parameters, signifying more flexible residues. While developing protocols for MD simulations, we evaluate the effects of running 1-microsecond long simulations and compare them to solution state NMR spectroscopy. If the overall tumbling time is removed from the simulation, then analysis blocks of 5-10 times the tumbling time is optimal to eliminate contributions from slower dynamics, which would not normally be measured in solution state NMR spectroscopy. We also assess the quality of the TIP4P(-EW) water model over TIP3P; although TIP4P simulates the isotropic tumbling time well for ecRNH, internal motions are equally not affected by either water model due to well-segregated motions. Additionally, the TIP4P water model does not appear to be able to replicate an axially symmetric shape for ecRNH (ecRNH is mostly spherical and only slightly axially symmetric). The final work of this thesis returns to the first overarching aim; we develop a specialized method that utilizes probability distribution functions to model spectral density functions. We derive the inverse Gaussian probability distribution function from general properties of spectral density functions at low and high frequencies for macromolecules in solution, using the principle of maximum entropy. The resulting model-free spectral density functions are finite at a frequency of zero and can be used to describe distributions of either overall or internal correlation times using the model-free ansatz. The approach is validated using 15N backbone relaxation data for the intrinsically disordered, DNA-binding region of the bZip transcription factor domain of the Saccharomyces cerevisiae protein GCN4, in the absence of cognate DNA.

<p>The history and philosophy underlying the design of the experimental component of an intensive introductory course in Nuclear Magnetic Resonance Spectroscopy (NMR) is presented. The concept of a " hands on " experience is used to transform the complete NMR novice into a competent operator. In addition to exposing the student to classical elucidation tools, advanced techniques, such as two dimensional and solid state NMR, are introduced. Through the use of unknowns, participants are encouraged to develop practical problem solving strategies. The detailed contents of the twenty-six experiments developed for the laboratory sessions are reviewed. The five day course schedule, and a coversheet, containing pertinent references for each experiment, is included. An examination of the unknowns utilized in the course, and a glossary of NMR terms is also presented. / Master of Science

Eutrophication is an increase in primary plant nutrients (Nitrogen [N] and Phosphorus [P]) in oceans, estuaries and lakes. The consequences of eutrophication are harmful algal blooms (HABs), resulting in algal toxin production and the depletion of oxygen as the extensive biomass decays. P is often the limiting nutrient and is viewed as a significant environmental problem. Most of the excess P that enters aquatic ecosystems originates from anthropogenic sources such as fertilizers, sewage, animal wastes, compost, crop residues, and wastewater. Over time, one of the main reservoirs of P becomes organic P (Po). We investigated the chemical nature and dynamics of P in cyanobacteria, horse manure, stormwater treatment areas, and rice fields. To better understand the chemical nature of P, the identification of specific P compounds was required, which was achieved through 31P nuclear magnetic resonance (NMR) spectroscopy. We investigated how paramagnetic metals and quadrupolar nuclei cause severe line broadening, peak shifts, and decreased the signal to noise ratio. Results revealed that certain Po forms are readily bioavailable to Microcystis aeruginosa. Additionally, the potential heterotrophic use of the organic portion (e.g., glucose, glycerol) of these P compounds are indicated for the growth and persistence of Microcystis aeruginosa. We showed that the cultivation of rice (Oryza sativa L.) had been found to effectively reduce P from agrarian soil and water through plant uptake and, therefore, minimizing downstream eutrophication. Soil, water, sugarcane, and rice plants at two different stages were analyzed for twelve different elements. Finally, we examined how a “relic” agrarian ditch in Stormwater Treatment Area 1 East (STA-1E) can be used for the retention and sequestration of P and other nutrients. The STAs were established to capture P from agricultural and other sources before reaching the Everglades. Retained P is primarily stored in the wetland soils and sediments, generated through a collection of interrelated physical, chemical, and biological processes. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

One- and two-dimensional NMR spectroscopy, including 13C{6Li}{1H} triple resonance techniques, were used to characterize a series of mixed alkyllithium aggregates and to study their exchange processes.

The 207Pb and 119Sn NMR chemical shift were used to study the effect of temperature on Ph3MCl (M= Pb and Sn) adducts in the presence of 10% excess pyridine. The 207Pb and 119Sn chemical shift indicate a slow exchange at low temperatures below -90 0C and a significant exchange at higher temperatures above 10 0C. A plot of temperature against 207Pb or 119Sn chemical shift showed a curve with gentle slope at lower and a steep slope at higher temperatures. A good linear correlation (coefficient. of 0.95) between Hammett substituent constant and 207Pb or 119Sn chemical shift of para-substituted derivatives of Ph3MCl.py* (py* = NMe2, OMe, Me, Ph, H, Br, COPh and COMe; at -90 0C in CD2Cl2/CH2Cl2) was found. Both 207Pb and 119Sn chemical shift ranges are characteristic of five coordinate systems resolving into trigonal bipyramidal geometry as shown by X-ray crystal structures. New complexes of the type [CpFe(CO)(SnPh3)L] (L = PPh3, PBu3, PCy3, PMe3, P(NMe2)3, PMePh2, PMe2Ph, P(p-FC6H5)3, P(p-OMeC6H4)3, P(p-tolyl)3, P(OMe)3, and P(OPh)3 were synthesized by ultraviolet irradiation of [CpFe(CO)2(SnPh3)] and the appropriate phosphine or phosphite ligand. 57Fe NMR studies of the complexes showed an increasing linear relationship with Tolman’s steric parameter, whereas with Tolman’s electronic parameter the 57Fe chemical shift showed a decrease. The X-ray crystallographic profile of the selected new piano stool type complexes shows a significant correlation to the NMR data (solution state), i.e. Fe-Sn, Fe-P bond length and Sn-Fe-P bond angle against chemical shifts of 207Pb and 119Sn. Disubstituted complexes of the type [CpFe(SnPh3)L2] (L = PMe3, PMe2Ph, P(OMe)3 and P(OPh)3 were synthesized under similar conditions as monosubstituted compounds. The correlation trends between the NMR data and X-ray crystallographic profiles are similar to those found for monocarbonylated complexes. Tungsten phosphine complexes of the type [W(CO)5(PR3)] (prepared from [W(CO)6] under thermal conditions) and [W(CO)4(NCMe)(PR3)] (prepared from [W(CO)5(PR3)] by use of Me3NO-promoted decarbonylation) were synthesized and characterized by, among other methods X-ray diffraction techniques (R = Ph, p-tolyl, p-OMeC6H4, p-FC6H4, p-CF3C6H4, and NMe2). The tungsten complexes [W(CO)4(NCMe)(PR3)] react with [(dppp)Pt{C≡C-C5H4N}2] at room temperature to form new complexes of the type [(dppe)Pt{C≡C-C5H4N-W(CO)4(PR3)}2] which were characterized unambiguously by NMR spectroscopy. There is a fair correlation between 195Pt and 183W NMR chemical shifts and Tolman’s electronic parameter which indicates a fair influence by the substituents of the phosphorus atom on both metal centres. Tungsten complexes of the type [W(CO)4(NCMe)(L)] (L= PPh3, P(p-FC6H4)3, P(p-OMeC6H4)3, P(p-tolyl)3, P(p-CF3C6H4)3, PMePh2, and PPh2(C6F5) react with [(PPh3)2Rh(H)2(pytca)] (pytca = 2-(4-pyridyl)thiazole-4-carboxylate) to form new complexes of the type [(PPh3)2Rh(H)2(pytca)- W(CO)4(L)] under mild conditions. These complexes were characterized principally by NMR spectroscopy and X-Ray crystallography (L = P(p-tolyl)3). Crystallographic evidence was found for π-π-π interactions involving two phenyl rings, one of the two phosphines bonded to rhodium atom, one of the three phosphines bonded to tungsten and the pyridyl ring of the thiazole corboxylate group. A second π-π interaction is found between a thiazole and a phenyl ring of the phosphine ligand bonded to the rhodium atom. A fair correlation was found between the rhodium and tungsten chemical shift measured from this series of complexes as a result of varied paraphenyl substituent of phosphine ligand bonded to the tungsten atom. This therefore implies the possible existence of electronic communication between the two bridged metal centres.

No description available.

No description available.

Soon after the importance of Nuclear Magnetic Resonance Spectroscopy was established more sophisticated instruments started coming into use. At present High Resolution Spectroscopes which are of the self-recording type are extensively used in research. However, the high cost of the instrument prevents its use in smaller and poorer schools. In recent years a low cost instrument of the single coil type has been constructed by the Aero Medical Laboratory which is alright for demonstration purposes but cannot be used for research because of low resolution. The idea of the present project was to see whether a similar instrument of double coil type could be made at a low cost of about $200. This instrument could give the proton resonance peak of water and be used for demonstration purposes.

No description available.

No description available.