Thèses sur le sujet « Nuclear magnetic resonance. Chemistry, Physical and theoretical »

This thesis describes the application of a wide variety of data processing methods, in particular the Maximum Entropy Method (MEM), to data from Nuclear Magnetic Resonance (NMR) experiments. Chapter 1 provides a brief introduction to NMR and to data processing, which is developed in chapter 2. NMR is described in terms of the classical model due to Bloch, and the principles of conventional (Fourier transform) data processing developed. This is followed by a description of less conventional techniques. The MEM is derived on several grounds, and related to both Bayesian reasoning and Shannon information theory. Chapter 3 describes several methods of evaluating the quality of NMR spectra obtained by a variety of data processing techniques; the simple criterion of spectral appearance is shown to be completely unsatisfactory. A Monte Carlo method is described which allows several different techniques to be compared, and the relative advantages of Fourier transformation and the MEM are assessed. Chapter 4 describes in vivo NMR, particularly the application of the MEM to data from Phase Modulated Rotating Frame Imaging (PMRFI) experiments. In this case the conventional data processing is highly unsatisfactory, and MEM processing results in much clearer spectra. Chapter 5 describes the application of a range of techniques to the estimation and removal of splittings from NMR spectra. The various techniques are discussed using simple examples, and then applied to data from the amino acid iso-leucine. The thesis ends with five appendices which contain historical and philosophical notes, detailed calculations pertaining to PMRFI spectra, and a listing of the MEM computer program.

A commercially available NMR spectrometer has been used to investigate fluid transport within porous solids. Two water-wet porous solids were investigated. The first was a sample of Fontainebleau sandstone, and the second was an idealised porous solid made from a random packing of glass beads. The samples were saturated with two immiscible phases, i.e. an oil and water phase. Pulsed field gradient (PFG) NMR measurements of one- and two-dimensional displacement probability distributions are reported, for steady-state flow and diffusion, within two phase saturated porous solids. Measurements were made with the porous solids prepare in different steady-state saturations. NMR relaxation measurements are also reported. Using the NMR data it was possible to evaluate the physical importance of parameters such as wettability and phase saturation on transport phenomena in two phase saturated porous solids. Various computer simulations were developed to model the experimental data.

Spin dynamics simulations are used to gain insight into important magnetic resonance experiments in the fields of chemistry, biochemistry, and physics. Presented in this thesis are investigations into how to accelerate these simulations by making them more efficient. Chapter 1 gives a brief introduction to the methods of spin dynamics simulation used in the rest of the thesis. The `exponential scaling problem' that formally limits the size of spin system that can be simulated is described. Chapter 2 provides a summary of methods that have been developed to overcome the exponential scaling problem in liquid state magnetic resonance. The possibility of utilizing the multiple processors prevalent in modern computers to accelerate spin dynamics simulations provides the impetus for the investigation found in Chapter 3. A number of different methods of parallelization leading to acceleration of spin dynamics simulations are derived and discussed. It is often the case that the parameters defining a spin system are time-dependent. This complicates the simulation of the spin dynamics of the system. Chapter 4 presents a method of simplifying such simulations by mapping the spin dynamics into a larger state space. This method is applied to simulations incorporating mechanical spinning of the sample with powder averaging. In Chapter 5, implementations of several magnetic resonance experiments are detailed. In so doing, use of techniques developed in Chapters 2 and 3 are exemplified. Further, specific details of these experiments are utilized to increase the efficiency of their simulation.

Nuclear magnetic resonance (NMR) is a popular spectroscopic method and has widespread use in many fields. Recent developments in solid-state NMR have increased interest in experiment and, alongside simultaneous developments in computational theory, have led to the field dubbed 'NMR crystallography.' This is a suite of methodologies, complementing the capabilities of other crystallographic methods in the determination of atomic structure, especially when large crystals cannot be made and when exploring materials with phenomena such as compositional, positional and dynamic disorder. NMR J-coupling is the indirect coupling between nuclear spins, which, when measured, can reveal a wealth of information about structure and bonding. This thesis develops and applies the method of Joyce for the prediction of NMR J-coupling in condensed matter systems using plane-wave pseudopotential density-functional theory, an important requirement for efficient treatment of finite and infinite periodic systems. It describes the first-ever method for the use of ultrasoft pseudopotentials and inclusion of special relativistic effects in J-coupling prediction, allowing for the treatment of a wider range of materials systems and overall greater user friendliness, thus making the method more accessible and attractive to the wider scientific community.

Nuclear magnetic resonance (NMR) is a powerful experimental technique for probing the local environment of nuclei in materials. However, it can be difficult to separate the large number of interactions that are recorded in the resulting spectra. First-principles calculations based on quantum mechanics therefore provide much-needed support for interpreting experimental spectra. In this way, the underlying mechanisms recorded in experimental spectra can be investigated on an atomic level, and trends can be noted with which to guide the direction of future experiments. This thesis presents two cases in which first-principles calculations do just that. The first is an investigation of the perovskite structures of NaNbO₃, KNbO₃, LiNbO₃ and the related solid solutions of Na_xK_1-xNbO₃, K_xNa_1-xNbO₃ and Li_xNa_1-xNbO₃ in order to study how structural disorder affects their NMR parameters. The second investigation involves the calculation of the Knight shift in platinum, palladium and rhodium---in their elemental bulk forms and in a set of surface structures. The Knight shift is a systematic shift in the NMR frequencies of metallic systems. It arises from the hyperfine interaction between the nuclear spins and the spins of the unpaired conduction electrons. When calculating the Knight shift, it is found that the Brillouin zone must be very finely sampled. A discussion of core polarisation is also presented. This is the polarisation of core electrons as a result of their interaction with valence electrons. In the case of Curie paramagnets, core polarisation can have a significant effect on the calculation of hyperfine parameters.

$\sp2$H-NMR is a powerful spectroscopic technique for investigating dynamics in solids. to extend the range of motional rates that can be quantitatively investigated, a new approach for measuring the quadrupolar spin-lattice relaxation time $T\sb{1Q}$ was developed. This uses a Broadband Jeener-Broekaert (BBJB) sequence with echo-detection, which avoids the frequency-discriminated excitation profile and spectral baseline distortion intrinsic to the conventional Jeener-Broekaert (JB) experiment. By combining the BBJB experiment with an Inversion-Recovery sequence with Quadrupole-Echo detection (IRQE), two independent longitudinal relaxation times, $T\sb{1Q}$ and $T\sb{1Z}$, can be measured. Spectral densities of motion $J\sb1(\omega\sb{o}$) and $J\sb2(2\omega\sb{o}$) are extracted from these relaxation times. The new approach was demonstrated on a nematic liquid crystal binary mixture of 4-methyl-4$\sp\prime$-cyanobiphenyl-d$\sb{11}$ (1CB) and 4-n-pentyl-4$\sp\prime$-cyanobiphenyl-d$\sb6$ (5CB). Measurements on mixtures containing 10 and 25 mol% 1CB revealed that rotational motion can be described by the third rate model and the correlation times and activation energies of 1CB and 5CB are concentration independent. In hexamethylbenzene, it was demonstrated that the orientation dependence of spectral densities provides geometric and kinetic information. This technique works well for motions which are in the fast regime ($k\ge10\sp7 s\sp{-1}$) and contribute to relaxation. at ambient temperature, the experimental data were fit by a simulation which included simultaneous threefold and sixfold rotations, with geometric distortions of the electric field gradient tensors of the methyl group. The best-fit jump rates for threefold methyl rotation was $k\sb3 = 5.0\times10\sp{11} s\sp{-1}$ and sixfold aromatic rotation was $k\sb6 = 3.85\times10\sp8 s\sp{-1}$, with out-of-plane and in-plane distortions of 2.5$\sp\circ$ and 1.2$\sp\circ$ respectively. Relaxation times of the bisphenol-A polycarbonate (BPA-PC) and its monomer (BPA) were measured between 250K to 400K. The data were fit to several dynamic models. Simple threefold methyl rotation accounts for the spectral density anisotropies of BPA but not those of the polymer BPA-PC. Inclusion of a semilogarithmic distribution of jump rates, $k\sb3$, improved the agreement qualitatively but not quantitatively. Modulation of threefold methyl jumps by libration of the $C\sb{3V}$ axis was treated with the Stochastic Liouville formalism. Best agreement is found if the two motions are correlated. Activation energies for methyl group rotation are 19.2 $\pm$ 2.0 kJ/mol and 13.0 $\pm$ 0.8 kJ/mol in monomer and polymer respectively.

Solid state 1H, 31P and 27Al Magic Angle Spinning (MAS) Nuclear Magnetic Resonance (NMR) was used in studies of surface species formed on a synthetic fluorapatite in aqueous suspensions at different pH with or without ions or ion complexes of iron or aluminium in the suspension. Different sites related to the PO43- ions at the mineral surface were suggested, POx, POxH and POxH2. Also, three sites formed of Ca2+, H+ and OH- ions at the fluorapatite surface CaOH2+, CaOH and Ca(OH) 2- were suggested. Both single-pulse and cross polarization MAS NMR experiments were used to measure the 1H, 31P and 27Al isotropic chemical shifts. In the 1H to 31P cross polarization experiments the contact time was varied in order to differentiate the resonance liners corresponding to different surface sites from the resonance lines assigned to the PO43- ions in the crystal structure of fluorapatite. In the solid state dipole-dipole recoupling MAS NMR experiments the sequence XY8-DRAMA was used in studies of distances between O,O'- dialkyldithiophosphates adsorbed on synthetic galena (PbS). The sequence was tested experimentally and gave highest double-quantum excitation efficiency of the tested dipole-dipole recoupling sequences tested at the spinning frequency 4.2 kHz. A new sequence IRS-DRAMA was derived analytically and showed high double quantum excitation efficiency in a broad interval of the 31P resonance frequencies at the spinning frequency 2.1 kHz.
Godkänd; 2006; 20061205 (haneit)

Symmetric division of Gram-negative bacteria depends on the combined action of three proteins that ensure correct positioning of the cell division septum; namely, MinC, MinD and MinE. To achieve this function, MinC and MinD form a membrane-bound complex that blocks cell division at all potential sites. Opposing this inhibition is MinE, which interacts with MinD via its N-terminal anti-MinCD domain to site-specifically counter the action of the MinCD complex. The anti-MinCD domain has been proposed to bind MinD in a helical conformation, however, little is actually known about the structure of this functionally critical region. In order to understand how MinE can perform its anti-MinCD function, we have therefore investigated the structural properties of the full-length MinE from N. gonorrhoeae. Results from solution NMR show that, in contrast to previous models, parts of the anti-MinCD domain are stably folded with many functionally important residues forming part of a beta-structure. In addition, this structure may be stabilized by interactions with the C-terminal topological specificity domain, since mutations made in one domain led to NMR spectral changes in both domains. The inactive MinE mutant L22D showed even larger evidence of structural perturbations, with significant destabilization of the entire MinE structure. Overall, these results suggest an intimate structural association between the anti-MinCD and topological specificity domains raising the possibility that the functional properties of the two domains could be modulated through this interaction.

This dissertation presents solid-state NMR studies of the chain conformation, dynamics and morphology of three adsorbed polymer systems: two random semi-crystalline copolymers, poly(ethylene-co-acrylic acid) (PEA) and poly(propylene-co-acrylic acid) (PPA), and an amorphous homopolymer, poly(n-butyl methacrylate) (PnBMA). Zirconia (ZrO2) was chosen as the substrate for all three polymers since the binding of carboxylic acids to this metal oxide is well understood. The choice of polymers was based on their particular bulk conformational and dynamic properties as well as their common use in polymer coatings. These studies are motivated by the general lack of a microscopic picture of adsorbed polymers, which can be provided by NMR, and the relevance of chain conformation and dynamics to important polymer film properties such as adhesion.
First the chain conformation and surface binding of adsorbed PEA as a function of acrylic acid content are characterized by 13C cross polarization - magic angle spinning (CP-MAS), 2D 1H- 13C wideline separation (WISE) and 1H spin diffusion NMR experiments and FTIR-PAS (Fourier transform infrared photoacoustic spectroscopy) measurements. The most important finding is that the chain conformation of adsorbed PEA is determined primarily by the sticker group density rather than the surface coverage. The second study of PEA concerns the chain dynamics in the bulk and adsorbed states. Variable temperature NMR experiments provide evidence that ethylene segments of adsorbed PEA form partially folded loops rather than flat extended trains. Finally 129Xe NMR studies, used to probe the morphology of adsorbed PEA, show a bulk-like signal only for the highest loadings.
The second system investigated, PPA, is another semi-crystalline random copolymer which binds to zirconia via carboxylate linkages. The 13 C CP-MAS NMR spectra of adsorbed PPAC unexpectedly show splittings normally associated with chain-chain packing in the crystalline regions of bulk polypropylene (PP). The splittings in the spectra of adsorbed PPAC, which are more resolved than in bulk PPA, are proposed to arise from recrystallization of the PP segments between sticker groups.
Finally the interfacial properties of an amorphous homopolymer, PnBMA were studied using 13C and 129Xe NMR to characterize adsorbed and filled samples. PnBMA binds to zirconia via the partial hydrolysis of the ester side chains. The remaining ester chains of adsorbed PnBMA are found to segregate to the polymer/air interface. Both adsorbed and ZrO 2-filled PnBMA show enhanced local segmental mobility. However, the 129Xe NMR measurements of the filled samples are consistent with restricted motion on a larger length scale which may be due to particle bridging.

In this work 23Na MAS NMR was validated as a successful quantitative method for studies of exchanging sodium in bentonites useful, in particular, for studies of ion-exchange kinetics. Na-enriched bentonites equilibrated in a re-circulated process water at iron-oxide pelletizing plants may acquire properties of Ca-bentonites after already 20 minutes of the equilibration time, since >50 % of sodium ions will be exchanged by calcium ions during first minutes of bentonite placed in contact with the process water. It was shown that all sodium activated bentonites used in this study exchange >50% of sodium in Na+/Ca2+ and ca 20 % of sodium in binary Na+/Mg2+ systems with the same bentonite/solution ratio and same concentrations of these ions in aqueous solutions as in the process water at a pelletizing plant. In total, approximately 50 % of the exchangeable sodium in original bentonites was exchanged after equilibrating of bentonites in the process water already after 20 minutes. Experimental Na+/Ca2+ exchange curves for ‘model’ Ca2+(aq) solutions and for process water are very similar as Ca2+ is the dominant constituent in the process water. Since bivalent ions (Ca2+ and Mg2+) that present in the process water readily replace Na+ ions, Na-bentonite transforms into Ca- or Mg- bentonite, which have worse rheological, swelling and, therefore, binding properties. This ion-exchange process can influence the binder performance in the pelletizing process. Taking into account that fluorapatite is one of the components present in a blend of minerals processed, possible interactions between orthophosphate (the principal anionic component of apatites) and bentonites in aqueous suspensions are considered. It was found that sorption of orthophosphate on Ca-montmorillonite follows a different pattern from sorption of orthophosphate on aluminum oxides and kaolinite. While there is a small amount of sorption below pH 7, which may involve inner-sphere complexation and precipitation of AlPO4 to Al-OH edge sites on the montmorillonite crystals, most sorption of orthophosphate occurs at higher pH. Both macroscopic sorption measurements and solid-state 31P MAS NMR suggest that above pH 7 there is precipitation of proton depleted calcium phosphate phases. Based on both 31P chemical shifts and 31P chemical shift anisotropies it was concluded that the principal precipitated phased are most likely ‘brushite-like’ phases. Very short spin-lattice T2(31P) relaxation times (≤100 μs) for the orthophosphate/bentonite systems can possibly be explained by the presence of paramagnetic Fe in bentonites. Since there are insufficient concentrations of soluble Fe species in the supernatant solution that may give rise to the observed effects, it is likely that orthophosphate is precipitated as thin layers on the surfaces of montmorillonite crystals, where phosphorus may interact with Fe atoms present in the crystal lattice. PO4-tetrahedra in sorbed species can be also distorted giving rise to a larger 31P CSA than for pure ‘apatite-like phases’. 29Si MAS and 1H-29Si CP/MAS NMR experiments on bentonite samples also performed in this work provide information about impurities of quartz in bentonites, a level of substitution of aluminum by iron atoms in the structure of montmorillonite and about the degree of hydration of montmorillonite. 29Si NMR experiments on bentonite incubated with waterglass in aqueous suspensions at concentrations of sodium silicates as in the process water demonstrated that one can follow the process of polymerization of waterglass in solutions and also detect sodium silicates polymerized on surfaces of bentonites already after 1 hour of incubation. Polymerized waterglass sorbed on bentonite surfaces may also alter rheological, swelling and, therefore, binding properties of sodium-activated bentonites used in pelletization of iron-oxide ores.

Godkänd; 2012; 20121011 (alegor); LICENTIATSEMINARIUM Ämne: Gränsytors kemi/Chemistry of Interfaces Examinator: Professor Oleg N. Antzutkin, Institutionen för samhällsbyggnad och naturresurser, Luleå tekniska universitet Diskutant: Professor emeritus Willis Forsling, Institutionen för samhällsbyggnad och naturresurser, Luleå tekniska universitet Tid: Onsdag den 5 december 2012 kl 13.00 Plats: C305, Luleå tekniska universitet

La theorie de la matrice de densite est utilisee pour obtenir une representation theoretique de la Resonance Magnetique Nucleaire (RMN) effectuee sur deux systemes differents, les deux menant a dence de "l'anisotropy orientational". Le premier cas examine la "Multiple Quantum Filtered" (MQF) ligne en forme de $ sp{23}$Na (I = 3/2) tel qu'observe recemment dans certains tissus biologiques. On peut remenquer la relaxation en utilisant la theorie de Redfield. La production de la contribution d'un tenseur de deuxieme ranq a la forme de la ligne est demontee etre directment attributable a la presence d'une constante de copulation quadrupole electrique qui ne disparant pas. Les equations des mouvements derivees pour I = 3/2 peuvent etre appliquees a une sequence general de pouls et une solution specifiques pour l'experience DQF est discutee. Le deuxieme cas recherche le signal reponse de o-D$ sb2$ (avec impulsion angulaire rotationalle J = 0 et le spin angulaire I = 2) et p-D$ sb2$ (avec J = 1 et I = 1) dans les experiences RMN consistant dans une sequence a deux pouls. L'amplitude prevue de l'echo solide pur les contributions de I = 1 et I = 2 est exprimee par une fraction molaire, les parametres du pouls, l'intervalle entre les deux pouls, le champs moyen dipolaire de la pair de spin et le champs non-homogene magnetique. Les proprietes de l'hydrogene solide sont discutees dans le contexte de l'experience de l'echo solide. Pour la fraction I = 2, les positions prevues pour les echos satellites sont determinees ainsi que l'impossibilite de les observer en D$ sb2$ solide est discutees en termes des granduers relative des constantes de copulation intramoleculaire et du champs non-homogene magnetique.

Reversible cis-trans isomerisation of a series of commercially interesting yellow azo dyes has been studied using the technique of Nuclear Magnetic Resonance (NMR) spectroscopy with in situ laser irradiation. Photostationary state (PSS) spectra of the azo dyes, provided by coupling laser irradiation into the sample within the probe of the NMR spectrometer, have allowed observation of azo cis isomer species that would otherwise elude detection and characterisation by NMR due to their rapid thermal decay times. The NMR results have been combined with geometry optimised structures obtained through ab initio (DFT) calculations in order to allow visualisation of the trans and cis isomer species, and explain NMR spectral features. In the majority of cases, these in vacuo calculated structures show a great deal of correlation with NMR observations of asymmetric, cis-trans isomerisation-induced chemical shift changes for protons adjacent to the azo bond. The cis isomer spectral pattern for substituted naphthyl group protons can hence be used as a diagnostic tool in determining the correct cis isomer conformation in molecules where more than one conformation may exist. In addition to the aforementioned characterisation studies, in situ irradiation has provided the opportunity to undertake a thorough investigation of the kinetics of photoand thermal isomerisation for the same yellow dye series. The results of these studies have been combined with previous work on similar systems to provide an extensive data set, and conduct analysis in a systematic fashion. Adding fibre-reactive groups, varying phenyl and chlorotriazine ring substituents, and altering naphthyl group sulfonation patterns have a profound effect on both the photochemical and thermal rates of isomerisation in these systems. In certain cases, the same structural calculations noted earlier have proved useful in rationalising the identified kinetic differences. The presence of phenyl substituents ortho to the azo bond has been shown to increase the rate of thermal cis isomer decay. Additionally, substituents bonded to a fibrereactive group distant from the azo bond have an appreciable effect on the barrier to thermal cis-trans isomerisation, but little effect on the photochemical characteristics of each isomer. Several sulfonated naphthyl group patterns have been studied, leading to an observation that sulfonate groups positioned ortho to the azo bond assist in retarding thermal isomerisation, with sulfonate groups in other positions having a much smaller effect. One particular molecule, a component of a currently available commercial dye, was studied for its interesting and previously unexplained behaviour, both photochemical and chemical. The dye demonstrated photoisomerisation at low concentrations only, with aggregation preventing formation of the cis isomer at higher concentrations. The trans isomer was found to undergo degradation to a product which did not photoisomerise. This product was identified as a benzotriazinium compound by multinuclear 2D correlation NMR spectroscopy, formed by a reversible cyclisation reaction involving the azo bond.

Sinefungin is an antibiotic and a close structural analog of S-adenosylmethionine, a co-factor for a vast number of enzymes. Sinefungin is one of a class of natural products containing both nucleoside and amino acid moieties. Sinefungin is a conformationally complex molecule. Because the sinefungin molecule consists of a planar adenine ring capable of both syn and anti orientation with respect to a conformationally mobile ribose ring and a flexible amino acid side chain, it has a wide range of conformational features that may be related to its bioactivity. Both lD and 2D F1NMR methods were used to evaluate vicinal proton coupling constants in order to determine probable dihedral angles about the C(2')-C(3') bond of the ribose ring and the C(α)-C(β), C(β)-C(γ), C(γ)-C(δ) and C(4') and C(5') dihedral angles of the amino acid side chain for proton spectra taken above pH 9.4. At this pH sinefungin is conformationally less flexible than S-adenosylmethionine. Overlapping resonances a detailed conformational analysis of sinefungin below pH 9.4. Most interesting was the discovery that the H(5') and H(5") resonances have the same chemical shift in acidic solutions so that valuable coupling constant information is lost. MM2 calculations were consistent with NMR results.

Magnetic fields influence the rate and/or yield of chemical reactions that proceed via spin correlated radical pair intermediates. The field of spin chemistry centres around the study of such magnetic field effects (MFEs). This thesis is particularly concerned with the effects of the weak magnetic fields B₀ ~ 1mT relevant in the ongoing debates on the mechanism by which animals sense the geomagnetic field and on the putative health effects of environmental electromagnetic fields. Relatively few previous studies have dealt with such weak magnetic fields. This thesis presents several new theoretical tools and applies them to interpret experimental measurements. Chapter 1 surveys the development and theory of spin chemistry. Chapter 2 introduces the use of Tikhonov and Maximum Entropy Regularisation methods as a new means of analysing MARY field effect data. These are applied to recover details of the diffusive motion of reacting pyrene and N,N-dimethylaniline radicals. Chapter 3 gives a fresh derivation and appraisal of an approximate, semiclassical approach to MFEs. Monte Carlo calculations allow the elucidation of several "rules of thumb" for interpreting MFE data. Chapter 4 discusses recent optically-detected zero-field EPR measurements, adapting the gamma-COMPUTE algorithm from solid state NMR for their interpretation. Chapter 5 explores the role of RF polarisation in producing MFEs. The breakdown in weak fields of the familiar rotating frame approximation is analysed. Chapter 6 reviews current knowledge and landmark experiments in the area of animal magnetoreception. The origins of the sensitivity of European robins Erithacus rubecula to the Earth’s magnetic field are given particular attention. In Chapter 7, Schulten and Ritz’s hypothesis that avian magnetoreception is founded on a radical pair mechanism (RPM) reaction is appraised through calculations in model systems. Chapter 8 introduces quantitative methods of analysing anisotropic magnetic field effects using spherical harmonics. Chapter 9 considers recent observations that European robins may sometimes be disoriented by minuscule RF fields. These are shown to be consistent with magnetoreception via a radical pair with no (effective) magnetic nuclei in one of the radicals.

Nessa tese de doutorado foram caracterizadas as configurações das tiossemicarbazonas do 2-formilpiridina (PATS2) e derivados no estado sólido e em solução utilizando as técnicas espectroscópicas Raman e ressonância magnética nuclear de hidrogênio (1H RMN). Utilizando os dados espectroscópicos obtidos foi possível obter informações da estereoquímica desses compostos. Verificamos que a substituição de alguns átomos de hidrogênio por grupos metilas causaram no caso particular do 4,4\' dimetil-tiossemicarbazona do 2-formilpiridina (DMePATS2), a estabilização do isômero Z ao invés do E. O estudo da caracterização desses compostos em solução mostrou que existe uma forte dependência da configuração presente em solução com o solvente. Essa dependência foi correlacionada com o valor de donor number dos solventes. Solventes com alto valor de donor number favorecem a formação de ligações de hidrogênio intermoleculares (composto-solvente) e, portanto, estabiliza o isômero E. Por outro lado, em solventes com menor valor de donor number, o isômero Z é estabilizado pela ligação de hidrogênio intramolecular. Comparando o efeito que os cátions alcalinos e alcalinos terrosos exercem sobre as configurações dos compostos PATS2 e DMePATS2, observamos novamente que os grupos metilas substituídos no N(4\') do DMePATS2 têm um papel importante nas propriedades desses compostos. No caso do PATS2 não ocorre a formação de complexos com esses metais em solução de ACN, esses cátions somente aumentam a velocidade da isomerização E-Z PATS2. Para o DMePATS2, ocorre a formação de complexos com os cátions estudados o que pode ser explicado pela presença dos grupos metílicos que aumentam a basicidade dos centros de coordenação da molécula favorecendo o ataque pelos cátions e estabilizando os complexos. Uma vez caracterizada as estruturas configuracionais predominantes no estado sólido e em solução, apresentamos a caracterização desses compostos adsorvidos em eletrodos utilizando nesse estudo a técnica SERS. Os resultados mostraram que a configuração do DMePATS2 adsorvido em eletrodo de prata depende do potencial aplicado ao eletrodo. Para potenciais negativos, a configuração predominante é E enquanto que para potenciais positivos existe quase que somente o isômero Z no eletrodo. A mudança no potencial aplicado ao eletrodo causa, portanto, isomerização E-Z reversível do DMePATS2 na superfície de prata. Verificamos que na presença de Mg2+ o isômero E DMePATS2 não é observado no eletrodo de prata devido a formação do complexo Mg2+-E-DMePATS2 em solução, ou seja, o complexo Mg2+-E-DMePATS2 não adsorve na superfície. Esse resultado indica que se a coordenação e a adsorção à superfície envolvem o mesmo sítio molecular, ocorre uma competição entre esses dois processos. No caso do 4-formilpiridina tiossemicarbazona (PATS4), os resultados SERS mostraram que variando o potencial aplicado ao eletrodo, não se observa nenhuma mudança significativa nos espectros em função do potencial indicando que não ocorre isomerização com o potencial, o que era esperado já que não existe possibilidade de formar ligação de hidrogênio intramolecular com o N do anel piridínico. Na presença de Mg2+ foi verificado que o complexo Mg2+-PATS4 adsorve na superfície do eletrodo. Devido às atividades biológicas desses compostos e aos diferentes mecanismos propostos na literatura, existe o interesse de conhecer os produtos da redução faradáica dos PATSn. Para isso, utilizamos a técnica SERS onde o potencial aplicado ao eletrodo é monitorado junto a um potenciostato acoplado a um registrador que indica o potencial de redução desses compostos. A espectroscopia na região do UV-Vis foi a técnica complementar usada na caracterização dos produtos faradáicos. Os resultados indicam que o 2-picolilamina e a tiouréia são os produtos de redução do PATS2. Um outro ponto de interesse desse trabalho foi a investigação do desempenho do 4-formilpiridina tiossemicarbazona (PATS4) como modificador de eletrodo para mediar a interação entre eletrodo de prata e o citocromo c (Cc). Nesse caso a técnica SERS, Raman intensificado pela superficie (λ0=632,8 nm) e a técnica SERRS, Raman Ressonante intensificado pela superficie (λ0=413,1 nm) foram utilizadas. A adição de Cc na solução eletrolítica não causou nenhuma mudança espectral nos modos vibracionais no espectro SERS do PATS4 que pudessem estar relacionadas à formação de ligação de hidrogênio entre a biomolécula e o modificador. Os espectros SERRS do Cc em eletrodos de prata modificados com PATS4 foram dependentes no entanto, com o potencial aplicado ao eletrodo indicando uma interação com o eletrodo. Em -0,4 V (vs. Ag/AgCl) são observadas as bandas características do Fe2+Cc em ca. 1368 e 1550 cm-1 e, quando oxidado a Fe3+Cc (+0,lV) essas bandas deslocam respectivamente para ca 1376 e 1562 cm-1. Sintetizamos o complexo [Ru(CN)5PATS4]3- e obtivemos os espectros SERS na presença e ausência de citocromo c. Como nesse complexo o N piridínico está ligado ao complexo de rutênio, não existe a possibilidade de formação de ligação de hidrogênio entre o anel piridínico do PATS4 e o citocromo c. Dessa maneira, se a interação entre o modificador e a biomolécula ocorresse por ligações de hidrogênio, deveríamos observar mudanças nos espectros SERS na região das bandas do estiramento do grupo C≡N. Os resultados desses experimentos não apresentaram nenhuma evidência quanto à formação de ligações de hidrogênio nesse sistema, o que indica que a interação entre o citocromo c e o [Ru(CN)5PATS4]3- seja eletrostática.
In this PhD thesis 2-formylpiridine thiosemicarbazone (PATS2) and derivatives configurations were characterized in the solid state and in solution using Raman and 1H Nuclear Magnetic Resonance (NMR) spectroscopies. Using spectroscopic data obtained from defined model solutions, information on the stereochemistry could be derived. It has been verified that the presence of the methyl groups in the N(4\') atom of DMePATS2 caused a stabilization of the Z isomer in the solid state instead of the stable E isomer in PATS2. Investigation in solution has shown a strong influence of the donor number of the solvents on the configuration of these compounds. Solvents with high donor numbers favor the formation of an intermolecular hydrogen bond between the solvent and the compound under investigation, thus stabilizing the E isomer. On the other hand, in solvents with low donor numbers, the Z isomer is stabilized due to intramolecular hydrogen bond. The methyl groups in DMePATS2 are also responsible for the different behavior of PATS2 and DMePATS2 in the presence of alkali and alkaline earth cations. Whereas in case of PATS2 these cations only catalyze the E-Z isomerization in ACN solution, complex formation between DMePATS2 and the cations was found to take place. The observed difference in behavior can be explained by an increase in the basicity of the coordination binding sites in DMePATS2 with respect to PATS2, which stabilizes the cation-DMePATS2 complexes. After characterization of the configuration of the compounds in the solid state and in solution, these molecules were adsorbed on a silver electrode and studied by SERS spectroscopy. The results have shown that the configuration of DMePATS2 adsorbed on the silver electrode depended on the applied potential. For negative potentials, the predominant configuration was E, while for positive potentials, almost only the Z isomer was found. In the presence of Mg2+ only the Z isomer of DMePATS2 was observed at any potential, which can be explained by the formation of Mg2+-E-DMePATS2 complex in solution. Additionally a comparison between the SERS result obtained for DMePATS2 and PATS4 (4-formylpyridine thiosemicarbazone) was made. In the case of PATS4, the SERS results have shown that there is no change in the spectra when the applied potential is varied; that could be related to an isomerization process, which was expected since there is no possibility of forming an intramolecular hydrogen bond in this compound. The SERS spectra of PATS4 in the presence of Mg2+ indicate the formation of the Mg2+ -PATS4 complex on the surface. The interest on the reduction products of these compounds concerns to the fact that they have a large spectrum of biological activities. Therefore they have been studied in more detail using SERS and UV-Vis spectroscopy. In the case of PATS2, 2-picolylamine and thiourea could be identified as reduction products of the electrochemical reaction. A further subject of interest was the investigation of the ability of 4-formylpyridine thiosemicarbazone (PATS4) to act as a surface modifier to mediate the interaction between a silver electrode and cytocrome c (Cc). In this case, SERS (λex = 632.8 nm) as well as surface enhanced resonance Raman scattering, SERRS (λex = 413 .1 nm) spectroscopy were used. Addition of Cc to the electrolytic solution did not induce spectral changes in the vibrational modes of SERS spectra of PATS4 that could be related to the formation of a hydrogen bond between the biomolecule and PATS4. Nevertheless, the SERRS spectra of Cc on modified silver electrode depended on the applied potential indicating an interaction with the electrode. At -0.4 V (vs. Ag/AgCl) the Fe2+Cc state marker bands at ca. 1368 and 1550 cm-1 were observed and, when oxidized to Fe3+Cc (+0.1V), these bands shifted to ca. 1376 and 1562 cm-1, respectively. SERS spectra of [Ru(CN)5PATS4]3- on the silver electrode were also obtained in presence and absence of Cc. In this complex, the pyridinic nitrogen is coordinated with Ruthenium complex. Therefore, the only possibility of forming hydrogen bond with Cc is through the C≡N group. The obtained results did not show any evidence that there is a hydrogen bond between Cc and this modifier. It is proposed that, in this case, the interaction governing the redox reaction is of electrostatic nature.

Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

The time-dependent visible spectra and the crystal structure of [Fe2(C20H24N8O2)(CH3CN)4]·PF6 (diketo-dimer) were studied. The spectra showed that the most significant chemistry occurred during the initial 1.5 hours of the synthetic reaction. The starting materials 343 nm peak shifted to a lower energy, at 360 nm, and a new shoulder appeared at 490 nm. This change suggests the formation of a new intermediate whose spectrum has an exceptional resemblance to the starting materials mixed valent species, [Fe2(TIED)(Cl)4]+1 (TIED = tetraiminethylene dimacrocycles). Two isosbestic points were found at 538 and 371 nm. The diketo-dimer's crystals appear to have individual colors, a physical characteristic called pleochroism. Pleochroism is a topic in the study of optical crystallography which is discussed and applied to the diketo-dimer. The extinction angle was estimated to be 14°, a value consistent for triclinic crystals. X-ray crystallography found that the diketo-dimer is triclinic, and has a space group of P-1. A noteworthy feature is the bond length, 1.406 Å, between the two linking bridgehead carbons. This bond length matches the value for partial double bonds of aromatic compounds. This argues for a delocalized electron circulating within the macrocycle. The NMR spectra of a diiron macrocycle, [Fe2(TIED)(CH3CN)4]4+, were examined. Temperature dependent, pH dependent, D+ substitution, selectively decoupled, and COSY 1H NMR experiments were performed. Two sets of structural equilibria were found. One set is temperature dependent, and the other is pH dependent. Of particular interest are the peaks centered at 9.7 ppm and assigned to the imine carbon protons H2. Its resonance indicates an imine proton in an extensively conjugated aromatic environment with an electron deficient metal.

Liquid chromatography is an essential technique in manufacturing biopharmaceuticals where it is used on all scales from analytical applications in R&D to full-scale production. In chromatography the target molecule, typically a protein, is separated and purified from other components and contaminants. Separation is based on different affinities of different molecules for the chromatographic medium and the physical and chemical properties of the latter determine the outcome. Controlling and designing those properties demand efficient analytical techniques. In this thesis the approach was to develop characterization methods based on nuclear magnetic resonance (NMR) spectroscopy for the assessment of various important physico-chemical properties. The rationale behind this strategy was that the versatility of NMR – with its chemical and isotopic specificity, high dynamic range, and direct proportionality between the integral intensity of the NMR signal and the concentration of spin-bearing atomic nuclei (e.g., 1H, 13C, 31P and 15N) – often renders it a very good choice for both qualitative and quantitative evaluations. These characteristics of NMR enabled us to develop two quantification methods for chromatography-media ligands, the functional groups that provide the specific interactions for the molecules being separated. Furthermore, a new method for measuring the distribution of macromolecules between the porous chromatographic beads and the surrounding liquid was established. The method, which we have named size-exclusion quantification (SEQ) NMR, utilizes the fact that it is possible to assess molecular size distribution from corresponding distribution of the molecular self-diffusion coefficient where the latter is accessible by NMR. SEQ-NMR results can also be interpreted in terms of pore-size distribution within suitable models. Finally, we studied self-diffusion of small molecules inside the pores of chromatographic beads. The results provided new insights into what affects the mass transport in such systems. The methods presented in this thesis are accurate, precise, and in many aspects better than conventional ones in terms of speed, sample consumption, and potential for automation. They are thus important tools that can assist a better understanding of the structure and function of chromatography media. In the long run, the results in this project may lead, via better chromatographic products, to better drugs and improved health.
Vätskekromatografi är en viktig teknik för tillverkning av biologiska läkemedel och används för alltifrån småskaliga analytiska applikationer till fullskalig produktion. I kromatografi separeras och renas målmolekylen (oftast ett protein), från andra komponenter och föroreningar genom att utnyttja molekylernas olika affinitet för det kromatografiska mediumet, vars fysikaliska och kemiska egenskaper har stor betydelse för hur separationen fungerar. För att kunna kontrollera och designa dessa egenskaper krävs effektiva analysmetoder. Strategin i den här avhandlingen var att utveckla metoder baserade på kärnmagnetisk resonans (NMR) spektroskopi för att karaktärisera flera viktiga fysikalisk-kemiska egenskaper. Anledningen till denna strategi är att mångsidigheten hos NMR – med dess kemiska och isotopiska specificitet, stora dynamiska omfång och direkta proportionalitet mellan NMR-signalens integralintensitet och koncentrationen av spinnbärande atomkärnor (t.ex. 1H, 13C, 31P och 15N) - ofta gör den till det bästa valet för både kvalitativa och kvantitativa tillämpningar. Dessa egenskaper hos NMR gjorde att vi kunde utveckla två kvantifieringsmetoder för kromatografimedia-ligander, dvs de funktionella grupperna som ger de specifika interaktioner som gör att molekylerna kan separeras. Dessutom har en ny metod för att mäta fördelningen av makromolekyler mellan de porösa kromatografiska pärlorna och den omgivande vätskan tagits fram. Metoden, som vi har valt att kalla size-exclusion quantification (SEQ) NMR, utnyttjar det faktum att det är möjligt att mäta molekylstorleksfördelningen genom att mäta motsvarande fördelning av självdiffusionskoefficienter, där den sistnämnda kan bestämmas med NMR. Resultaten från SEQ-NMR kan tolkas i termer av porstorleksfördelningar genom att använda lämpliga modeller. Slutligen studerade vi självdiffusion av små molekyler inuti porerna i kromatografiska pärlor. Resultaten gav nya insikter om vad som påverkar masstransporten i sådana system. De metoder som presenteras i denna avhandling är noggranna, precisa och på många sätt bättre än konventionella metoder när det gäller hastighet, låg provförbrukning och automatiseringspotential. De nya metoderna är därför viktiga verktyg som kan hjälpa till att ge en bättre förståelse av struktur och funktion hos kromatografimedia. I det långa loppet kan resultat från det här projektet kunna bidra till effektivare kromatografiska produkter, vilket i slutändan kan leda till bättre läkemedel och hälsa.

QC 20170403

This thesis is about using nuclear magnetic resonance (NMR) spectroscopy for studying soft materials. Soft materials may be encountered everyday by most readers of this thesis, for example when taking a shower or watching TV. The usefulness of these materials originates from them being soft yet, at the same time, having some kind of a structure. The characteristic length scale of those structures is often on the order of nanometers (10-9 m) and the structure can respond to various external stimuli such as temperature, electric and magnetic fields, or the presence of interfaces. NMR spectroscopy excels when studying soft materials because it is a non-invasive technique with a large spectral resolution. Moreover, different NMR methods allow us to study local molecular dynamics or longer-range translational diffusion. Understanding those latter aspects is very important for the development of dynamic and responsive materials. Papers I-III present our work on assessing molecular adsorption on interfaces in colloidal dispersions. Here, carbon nanotubes (CNTs) or silica particles were the colloidal substrates to which proteins, polymers or surfactants adsorbed. Papers IV-VI concern ionic mobility in liquid crystals (LCs). The influence of material structure on, for example, the anisotropy of diffusion or on the association/dissociation of ions was studied in several LC phases.
QC 20110225

Protein tertiary structure is more conserved than amino acid sequence, leading to a diverse range of functions observed in the same fold. Despite < 20 % overall sequence identity, cytochromes P450 all have the same fold. Bacterial Class I P450s receive electrons from a highly specific, often unidentified, ferredoxin, in which case the hemoprotein is termed “orphaned”. CYP199A2, a Class I P450, accepts electrons from ferredoxins Pux and HaPux. Five orientation-dependent and one orientation-independent DEER measurements on paramagnetic HaPux and spin-labelled CYP199A2 yielded vector restraints, which were applied to building a model of the CYP199A2:HaPux complex in silico. A different binding mode was observed compared to P450cam:Pdx and P450scc:Adx, both recently elucidated by X-ray crystallography. This protocol was also applied to the CYP101D1:Arx complex. The first three measurements indicate that this heterodimer does not have a similar orientation to CYP199A2:HaPux, P450cam:Pdx, or P450scc:Adx. P450cam was fused to putidatredoxin reductase (PdR) to explore the kinetic effects with a view to improving electron transfer to orphan P450s. Heme incorporation of this enzyme depends on linker length. In whole cells, the fusion was more active after longer incubations. In vitro kinetics of the fusion exhibited some co-operativity and enhanced kinetics over the unfused system under steady-state conditions. The putative iron-sulfur biosynthesis ferredoxin PuxB had been engineered by rational mutagenesis to support catalysis by CYP199A2. It was confirmed this arose from improved protein-protein recognition. Engineering of E. coli ferredoxin based on these findings was carried out, resulting in electron-transfer to CYP199A4 from a novel engineered alien ferredoxin.

Conventional computing faces a huge technical challenge as traditional transistors will soon reach their size limitations. This will halt progress in reaching faster processing speeds and to overcome this problem, require an entirely new approach. Quantum computing (QC) is a natural solution offering a route to miniaturisation by, for example, storing information in electron or nuclear spin states, whilst harnessing the power of quantum physics to perform certain calculations exponentially faster than its classical counterpart. However, QCs face many difficulties, such as, protecting the quantum-bit (qubit) from the environment and its irreversible loss through the process of decoherence. Hybrid systems provide a route to harnessing the benefits of multiple degrees of freedom through the coherent transfer of quantum information between them. In this thesis I show coherent qubit transfer between electron and nuclear spin states in a ¹⁵N@C₆₀ molecular system (comprising a nitrogen atom encapsulated in a carbon cage) and a solid state system, using phosphorous donors in silicon (Si:P). The propagation uses a series of resonant mi- crowave and radiofrequency pulses and is shown with a two-way fidelity of around 90% for an arbitrary qubit state. The transfer allows quantum information to be held in the nuclear spin for up to 3 orders of magnitude longer than in the electron spin, producing a ¹⁵N@C₆₀ and Si:P ‘quantum memory’ of up to 130 ms and 1.75 s, respectively. I show electron and nuclear spin relaxation (T₁), in both systems, is dominated by a two-phonon process resonant with an excited state, with a constant electron/nuclear T₁ ratio. The thesis further investigates the decoherence and relaxation properties of metal atoms encapsulated in a carbon cage, termed metallofullerenes, discovering that exceptionally long electron spin decoherence times are possible, such that these can be considered a viable QC candidate.

There is a general lack of atomic resolution data of mobile regions of membrane proteins embedded in lipid bilayers. As an inherently complex system, few techniques can capture information about the mobile portions of an otherwise immobilized protein. The nature of crystallography and solid-state NMR relies on structural rigidity. Solution-state NMR relies on overall mobility of a protein for resolution. In the middle regime, there are few solutions to study these systems. The inward-rectifying, pH-gated potassium channel KcsA from Streptomyces lividans makes an excellent model for the development of methods to study mobile regions of membrane proteins. Of its 160 residues, more than a third are in extracellular do- mains and are not typically captured by solid-state NMR or crystallographic techniques. These pages present evidence that KcsA’s C-terminus is highly mobile and becomes increasingly dynamic when the protein is at low pH and high K+ concen- tration, where the channel is known to be active. By applying proton-detected, high-resolution magic angle spinning NMR (HR-MAS) to fractionally deuterated KcsA, previously unattainable correlations are collected and new resonance assignments are made, demonstrating the utility of the technique. The lipid environment is well known to regulate the function of KcsA in particular and membrane proteins in general. It is generally assumed that reconstituting KcsA into a synthetic phospholipid membranes provides the protein a well-defined environment. Data is presented here which shows that KcsA co-purifies with phosphoglycerol lipids from the E. coli membrane and that these molecules are 13C enriched in the course of isotopically labeling KcsA. Further, significant hydrolysis of both co- purifying and synthetic lipids occurs under ordinary experimental conditions. These findings demand that routine analysis of samples must include verification of the chemical integrity of lipids. Finally, the feasibility of applying dynamic nuclear polarization-enhanced NMR (DNP) to KcsA is investigated as a means of elucidating information about its termini. Although KcsA is known to enhance poorly by DNP, data presented here show that this is not an intrinsic property of the protein but rather an effect of the matrix in which KcsA is investigated. The use of a 15N-enriched free amino acid dissolved into buffers used for DNP is shown to be a powerful diagnostic internal standard.

Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2008.
Source: Dissertation Abstracts International, Volume: 69-11, Section: B, page: 6759. Adviser: Chad M. Rienstra. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

abstract: Structural details of phosphonic acid functionalized nanomaterials and protic ionic liquids (PILs) were characterized using nuclear magnetic resonance (NMR) spectroscopy. It is well known that ligands play a critical role in the synthesis and properties of nanomaterials. Therefore, elucidating the details of ligand-surface and ligand-ligand interactions is crucial to understanding nanomaterial systems more completely. In an effort to further the understanding of ligand-surface interactions, a combination of multi-nuclear (1H, 29Si, 31P) and multi-dimensional solid-state NMR techniques were utilized to characterize the phosphonic acid functionalization of fumed silica nanoparticles using methyl phosphonic acid (MPA) and phenyl phosphonic acid (PPA). Quantitative 31P MAS solid-state NMR measurements indicate that ligands favor a monodentate binding mode. Furthermore, 1H-1H single quantum-double quantum (SQ-DQ) back-to-back (BABA) 2D NMR spectra of silica functionalized with MPA and PPA indicate that the MPA and PPA are within 4.2±0.2 Å on the surface of the nanomaterial. The ligand capping of phosphonic acid (PA) functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of ligand exchange, solution and solid-state 31P NMR spectroscopy. In order to quantify the ligand populations on the surface of the QDs, ligand exchange facilitated by PPA resulted in the displacement of the PAs, and allowed for quantification of the free ligands using 31P liquid state NMR. In addition to characterizing nanomaterials, the ionicity and transport properties of a series of diethylmethylamine (DEMA) based protic ionic liquids (PILs) were characterized, principally utilizing NMR. Gas phase proton affinity was shown to be a better predictor for the extent of proton transfer, and in turn the ionicity of the PIL, than using ∆pKa. Furthermore, pulsed field gradient (PFG) NMR was used to determine that the exchangeable proton diffuses with the cation or the anion based on the strength of the acid used to generate the PILs.
Dissertation/Thesis
Doctoral Dissertation Chemistry 2015

Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2007.
Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 1027. Adviser: Chad M. Rienstra. Includes supplementary digital materials. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

abstract: Nanomaterials have attracted considerable attention in recent research due to their wide applications in various fields such as material science, physical science, electrical engineering, and biomedical engineering. Researchers have developed many methods for synthesizing different types of nanostructures and have further applied them in various applications. However, in many cases, a molecular level understanding of nanoparticles and their associated surface chemistry is lacking investigation. Understanding the surface chemistry of nanomaterials is of great significance for obtaining a better understanding of the properties and functions of the nanomaterials. Nuclear magnetic resonance (NMR) spectroscopy can provide a familiar means of looking at the molecular structure of molecules bound to surfaces of nanomaterials as well as a method to determine the size of nanoparticles in solution. Here, a combination of NMR spectroscopic techniques including one- and two-dimensional NMR spectroscopies was used to investigate the surface chemistry and physical properties of some common nanomaterials, including for example, thiol-protected gold nanostructures and biomolecule-capped silica nanoparticles. Silk is a natural protein fiber that features unique properties such as excellent mechanical properties, biocompatibility, and non-linear optical properties. These appealing physical properties originate from the silk structure, and therefore, the structural analysis of silk is of great importance for revealing the mystery of these impressive properties and developing novel silk-based biomaterials as well. Here, solid-state NMR spectroscopy was used to elucidate the secondary structure of silk proteins in N. clavipes spider dragline silk and B. mori silkworm silk. It is found that the Gly-Gly-X (X=Leu, Tyr, Gln) motif in spider dragline silk is not in a β-sheet or α-helix structure and is very likely to be present in a disordered structure with evidence for 31-helix confirmation. In addition, the conformations of the Ala, Ser, and Tyr residues in silk fibroin of B. mori were investigated and it indicates that the Ala, Ser, and Tyr residues are all present in disordered structures in silk I (before spinning), while show different conformations in silk II (after spinning). Specifically, in silk II, the Ala and Tyr residues are present in both disordered structures and β-sheet structures, and the Ser residues are present primarily in β-sheet structures.
Dissertation/Thesis
Doctoral Dissertation Chemistry 2017

abstract: The physiological phenomenon of sensing temperature is detected by transient receptor (TRP) ion channels, which are pore forming proteins that reside in the membrane bilayer. The cold and hot sensing TRP channels named TRPV1 and TRPM8 respectively, can be modulated by diverse stimuli and are finely tuned by proteins and lipids. PIRT (phosphoinositide interacting regulator of TRP channels) is a small membrane protein that modifies TRPV1 responses to heat and TRPM8 responses to cold. In this dissertation, the first direct measurements between PIRT and TRPM8 are quantified with nuclear magnetic resonance and microscale thermophoresis. Using Rosetta computational biology, TRPM8 is modeled with a regulatory, and functionally essential, lipid named PIP2. Furthermore, a PIRT ligand screen identified several novel small molecular binders for PIRT as well a protein named calmodulin. The ligand screening results implicate PIRT in diverse physiological functions. Additionally, sparse NMR data and state of the art Rosetta protocols were used to experimentally guide PIRT structure predictions. Finally, the mechanism of thermosensing from the evolutionarily conserved sensing domain of TRPV1 was investigated using NMR. The body of work presented herein advances the understanding of thermosensing and TRP channel function with TRP channel regulatory implications for PIRT.
Dissertation/Thesis
Doctoral Dissertation Biochemistry 2018

abstract: Spider dragline silk is well known for its outstanding mechanical properties - a combination of strength and extensibility that makes it one of the toughest materials known. Two proteins, major ampullate spidroin 1 (MaSp1) and 2 (MaSp2), comprise dragline silk fibers. There has been considerable focus placed on understanding the source of spider silk's unique mechanical properties by investigating the protein composition, molecular structure and dynamics. Chemical compositional heterogeneity of spider silk fiber is critical to understand as it provides important information for the interactions between MaSp1 and MaSp2. Here, the amino acid composition of dragline silk protein was precisely determined using a solution-state nuclear magnetic resonance (NMR) approach on hydrolyzed silk fibers. In a similar fashion, solution-state NMR was applied to probe the "13"C/"15"N incorporation in silk, which is essential to understand for designing particular solid-state NMR methods for silk structural characterization. Solid-state NMR was used to elucidate silk protein molecular dynamics and the supercontraction mechanism. A "2"H-"13"C heteronuclear correlation (HETCOR) solid-state NMR technique was developed to extract site-specific "2"H quadrupole patterns and spin-lattice relaxation rates for understanding backbone and side-chain dynamics. Using this technique, molecular dynamics were determined for a number of repetitive motifs in silk proteins - Ala residing nanocrystalline &beta-sheet; domains, 3"1"-helical regions, and, Gly-Pro-Gly-XX &beta-turn; motifs. The protein backbone and side-chain dynamics of silk fibers in both dry and wet states reveal the impact of water on motifs with different secondary structures. Spider venom is comprised of a diverse range of molecules including salts, small organics, acylpolyamines, peptides and proteins. Neurotoxins are an important family of peptides in spider venom and have been shown to target and modulate various ion channels. The neurotoxins are Cys-rich and share an inhibitor Cys knot (ICK) fold. Here, the molecular structure of one G. rosea tarantula neurotoxin, GsAF2, was determined by solution-state NMR. In addition, the interaction between neurotoxins and model lipid bilayers was probed with solid-state NMR and negative-staining (NS) transmission electron microscopy (TEM). It is shown that the neurotoxins influence lipid bilayer assembly and morphology with the formation of nanodiscs, worm-like micelles and small vesicles.
Dissertation/Thesis
Ph.D. Chemistry 2014

This dissertation focuses on a very special topic in the field of Nuclear Magnetic Resonance (NMR) in solution: Intermolecular Multiple Quantum Coherences, or iMQCs, which can only be created by intermolecular dipolar couplings. Since the very beginnings of NMR, it has been known that dipolar couplings dominate the solid-state linewidth for spin-1/2 nuclei, but the effects are still not fully understood. The angular dependency (1-3cos2θij) and distant dependency (rij-3) of dipolar coupling led to an oversimplified conclusion that it can be ignored in an isotropic liquid. Thus, it was surprising when COSY Revamped by Asymmetric Z-gradient Echo Detection (CRAZED) was first introduced in the early `90s and showed strong iMQC signals. Since then, CRAZED has inspired a wide range of applications for iMQCs and led to two different but equivalent mathematical frameworks to describes these effects, which we call the conventional DDF theory.

However, several disagreements between the conventional DDF theory and experiments have grasped our attention recently. This dissertation will: first, demonstrate how conventional picture fails by two examples, Multi-axis CRAZED (MAXCRAZED) and Gradient-embedded COSY Experiment (GRACE); second, provide a corrected DDF theory; and, third, discuss what impact this correction will bring.

Intermolecular double quantum coherences (iDQCs) are very sensitive to the local anisotropy (10μm - 1mm) and can be used to create positive contrast highlighting superparamagnetic iron oxide nanoparticles (SPIONs). This dissertation will show the design and optimization of iDQC anisotropy by a series of phantom experiments. A set of numerical simulations will then be provided for a sub-voxel level explanation. We will also demonstrate how the newly corrected DDF theory can be quickly adapted to improve the iDQC anisotropy.

Finally, as a side product of this research, the mechanism of diacetyl hydration/dehydration as solved by NMR will be provided.

Dissertation